https://www.slicer.org/w/api.php?action=feedcontributions&feedformat=atom&user=Vmagnotta Slicer Wiki - User contributions [en] 2026-05-05T11:55:56Z User contributions MediaWiki 1.33.0 https://www.slicer.org/w/index.php?title=Modules:BRAINSFit&diff=14487 Modules:BRAINSFit 2010-04-27T19:58:41Z <p>Vmagnotta: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Module Name=== MyModule {| |[[Image:screen…'</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===Module Name===<br /> MyModule<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive or CLI<br /> <br /> Category: Base or (Filtering, Registration, ''etc.'')<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Author1: Affiliation &amp; logo, if desired<br /> * Contributor1: Affiliation &amp; logo, if desired<br /> * Contributor2: Affiliation &amp; logo, if desired<br /> * Contact: name, email<br /> <br /> ===Module Description===<br /> Overview of what the module does goes here.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> This module is especially appropriate for these use cases:<br /> <br /> * Use Case 1:<br /> * Use Case 2:<br /> <br /> Examples of the module in use:<br /> <br /> * Example 1<br /> * Example 2<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * Tutorial 1<br /> ** Data Set 1<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> A list panels in the interface, their features, what they mean, and how to use them. For instance:<br /> <br /> {|<br /> |<br /> * '''Input panel:'''<br /> ** '''First input'''<br /> ** '''Second input'''<br /> * '''Parameters panel:'''<br /> ** '''First parameter'''<br /> ** '''Second parameter'''<br /> * '''Output panel:'''<br /> ** '''First output'''<br /> ** '''Second output'''<br /> * '''Viewing panel:'''<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> Other modules or packages that are required for this module's use.<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br /> * MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> Links to the module's source code:<br /> <br /> Source code:<br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> Include funding and other support here.<br /> <br /> ===References===<br /> Publications related to this module go here. Links to pdfs would be useful.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:BRAINSDemonWarp&diff=14486 Modules:BRAINSDemonWarp 2010-04-27T19:58:19Z <p>Vmagnotta: Created page with 'Return to Slicer 3.6 Documentation Gallery of New Features __NOTOC__ ===Module Name=== MyModule {| |[[Image:screen…'</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===Module Name===<br /> MyModule<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive or CLI<br /> <br /> Category: Base or (Filtering, Registration, ''etc.'')<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Author1: Affiliation &amp; logo, if desired<br /> * Contributor1: Affiliation &amp; logo, if desired<br /> * Contributor2: Affiliation &amp; logo, if desired<br /> * Contact: name, email<br /> <br /> ===Module Description===<br /> Overview of what the module does goes here.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> This module is especially appropriate for these use cases:<br /> <br /> * Use Case 1:<br /> * Use Case 2:<br /> <br /> Examples of the module in use:<br /> <br /> * Example 1<br /> * Example 2<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * Tutorial 1<br /> ** Data Set 1<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> A list panels in the interface, their features, what they mean, and how to use them. For instance:<br /> <br /> {|<br /> |<br /> * '''Input panel:'''<br /> ** '''First input'''<br /> ** '''Second input'''<br /> * '''Parameters panel:'''<br /> ** '''First parameter'''<br /> ** '''Second parameter'''<br /> * '''Output panel:'''<br /> ** '''First output'''<br /> ** '''Second output'''<br /> * '''Viewing panel:'''<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> Other modules or packages that are required for this module's use.<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br /> * MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> Links to the module's source code:<br /> <br /> Source code:<br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> Include funding and other support here.<br /> <br /> ===References===<br /> Publications related to this module go here. Links to pdfs would be useful.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=14354 Documentation/3.6 2010-04-27T02:17:33Z <p>Vmagnotta: /* Wizards */</p> <hr /> <div>This is work in progress<br /> <br /> =Main GUI=<br /> <br /> *[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak) <br /> *[[Modules:EventBindings-3.6| &quot;Hot-keys&quot; and Keyboard Shortcuts]] (Wendy Plesniak) <br /> *[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br /> *[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br /> *[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)<br /> *[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)<br /> <br /> =Modules=<br /> *Please copy the template linked below, paste it into your page and customize it with your module's information.<br /> [[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]] <br /> *See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br /> *To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br /> <br /> Please adhere to the naming scheme for the module documentation:<br /> *[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br /> <br /> =Requirements for Modules=<br /> {| border=&quot;00&quot; cellpadding=&quot;5&quot; cellspacing=&quot;0&quot;<br /> |-<br /> | rowspan=&quot;2&quot;| <br /> * The module is '''feature complete''', it does everything that it advertises it can do<br /> * The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br /> * Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.<br /> *Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.<br /> * The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]<br /> ** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br /> ** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons. <br /> ** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)<br /> * Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.<br /> * Follow [[Documentation-3.5-Rons-Rules|'''Ron's rules for tools''']]<br /> | style=&quot;background: #e5e5e5&quot; align=&quot;center&quot;| Examples for the Help and <br /> Acknowledgment Panels<br /> |-<br /> | style=&quot;background: #ebeced&quot;|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br /> |}<br /> <br /> =List of Modules added or significantly revised since the 3.4 release=<br /> * Interactive Editor<br /> * Volume Rendering<br /> * Colors (Nicole Aucoin)<br /> * MRI Bias Field Correction (Sylvain Jaume)<br /> * 4D Image (Viewer) (Junichi Tokuda)<br /> * 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)<br /> * Fast Marching segmentation (Andriy Fedorov)<br /> * Mesh Contour Segmentation (Peter Karasev)<br /> * Subvolume extraction with ROI widget (Andriy Fedorov)<br /> * Registration Metrics (HD and DSC) (Haytham Elhawary)<br /> * Measurements (rulers and angles) (Nicole Aucoin)<br /> * Affine registration (Casey Goodlett)<br /> * Collect Patient Fiducials (Andrew Wiles)<br /> * IGT Tool Selector (Andrew Wiles)<br /> * Fiducials (Nicole Aucoin)<br /> * PETCTFusion (Wendy Plesniak)<br /> * N4 Bias Field Correction (Andriy Fedorov)<br /> <br /> =List of Modules=<br /> ==Core==<br /> *[[Slicer3:Multiple_Cameras| Camera Module]] (Sebastian Barre)<br /> *[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)<br /> *[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) <br /> **[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)<br /> *[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich) <br /> *[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin) <br /> *[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)<br /> *[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich) <br /> *[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller) <br /> *[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin) <br /> *[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6&lt;/font&gt;<br /> *[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich) <br /> *[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)<br /> *[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)<br /> <br /> ==Specialized Modules==<br /> <br /> Please adhere to the naming scheme for the module documentation:<br /> *[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br /> <br /> ===Wizards===<br /> *[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)<br /> *[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta)<br /> <br /> ===Informatics Modules===<br /> *[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus) <br /> *[[Modules:QDECModule-Documentation-3.6| QDEC Module]] (Nicole Aucoin) <br /> *[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)<br /> <br /> ===Registration===<br /> *[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.<br /> *Fast<br /> **[[Modules:Transforms-Documentation-3.6|Transforms Module]]: manual &amp; interactive rigid registration , (Alex Yarmarkovich)<br /> **[[Modules:AffineRegistration-Documentation-3.4|Fast Affine Module]]: automated fast affine registration , (Daniel Blezek) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6&lt;/font&gt;'<br /> **[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Non-rigid BSpline Module]]: fast non-rigid registration , (Bill Lorensen) <br /> *Robust<br /> **[[Modules:RegisterImages-Documentation-3.6|Robust Rigid-Affine-Nonrigid Module]]: registration with robust initialization, variable DOF and masking options, (Casey Goodlett)<br /> **[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Module]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content , (Casey Goodlett)<br /> *Brain Only<br /> **[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform Module]]: align a single brain along AC-PC line , (Nicole Aucoin)<br /> *Non-Raster-Image Data<br /> **[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration Module]]: align two sets of fiducials (translation, rigid or similarity) (Casey Goodlett)<br /> **[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration Module]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6 (in progress)&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6 (in progress)&lt;/font&gt;<br /> *Experimental and auxiliary<br /> **[[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6&lt;/font&gt;<br /> **[[Modules:LinearRegistration-Documentation-3.4|Linear Registration Module]]: (fast) rigid registration m (Daniel Blezek) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6&lt;/font&gt;<br /> <br /> ===Segmentation===<br /> *[[Modules:SegmentationOverview3.6|Overview]]<br /> **[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl) <br /> **[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl) <br /> **[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl) <br /> **[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)<br /> **[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)<br /> **[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6&lt;/font&gt;<br /> **[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).<br /> <br /> ===Statistics===<br /> *[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)<br /> <br /> ===Diffusion MRI===<br /> *Diffusion MRI<br /> ** DWI filtering<br /> ***[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) <br /> ***[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) <br /> ***[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) <br /> ** Diffusion tensor utilities<br /> ***[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar) <br /> ***[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) <br /> ** Resampling<br /> ***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)<br /> ** Tractography<br /> ***[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar) <br /> ***[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) <br /> ***[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich) <br /> ***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal) <br /> ***[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)<br /> <br /> ===IGT===<br /> *[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)<br /> *[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)<br /> *[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)<br /> *[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)<br /> *[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)<br /> <br /> ===Time Series===<br /> * [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)<br /> <br /> ===Filtering===<br /> *[[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)<br /> *[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)<br /> *[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] '''In progress''' (Bill Lorensen, Xiaodong Tao)<br /> *[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich) <br /> *[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)<br /> *[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)<br /> *[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)<br /> *[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen) <br /> *Arithmetic<br /> **[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan) <br /> **[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan) <br /> ** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin) <br /> ** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin, Harini Veeraraghavan) <br /> *Denoising<br /> **[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6&lt;/font&gt;<br /> **[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6&lt;/font&gt;<br /> **[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6&lt;/font&gt;<br /> **[[Modules:MedianFilter-Documentation-3.6|Median Filter]] '''In progress''' (Xiaodong Tao) <br /> *Morphology<br /> **[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Jim Miller) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6&lt;/font&gt;<br /> **[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)<br /> **[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)<br /> <br /> ===Surface Models===<br /> *[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin) <br /> *[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6&lt;/font&gt;<br /> *[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev) <br /> *[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6 (in progress)&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6 (in progress)&lt;/font&gt;<br /> *[[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6 (in progress)&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6 (in progress)&lt;/font&gt;<br /> *[[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6 (in progress)&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6 (in progress)&lt;/font&gt;<br /> *[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich) <br /> *[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)<br /> <br /> ===Batch processing===<br /> *[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)<br /> *[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)<br /> *[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)<br /> *[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)<br /> <br /> ===Converters===<br /> *[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao) <br /> *[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] '''(in progress)''' (Xiaodong Tao)<br /> *[[Modules:OrientImages-Documentation-3.6|Orient Images]] '''(In progress)''' (Xiaodong Tao) <br /> *[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) &lt;span style=&quot;background:hotpink; color:white&quot;&gt;Not yet 3.6 (in progress)&lt;/span&gt;&lt;font background=hotpink color=white&gt;Not yet 3.6 (in progress)&lt;/font&gt;<br /> *[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)<br /> <br /> ==Experimental==<br /> * [[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] '''(in progress)''' (Andriy Fedorov)<br /> <br /> =Slicer Extensions=<br /> <br /> ==Extensions for Downloading==<br /> ===Introduction===<br /> [[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]<br /> * Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.<br /> * Some of the extensions do not use the Slicer license. Please review carefully.<br /> * For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.<br /> * The version that is available through the extension manager is chosen by the developer of that extension <br /> <br /> We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.<br /> Click [http://www.nitrc.org/search/?type_of_search=soft&amp;words=slicer3&amp;Search.x=0&amp;Search.y=0&amp;Search=Search here] to see a listing of Slicer 3 extensions on NITRC.<br /> <br /> [[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br /> To add extension modules to an installed binary of slicer:<br /> * Use the View-&gt;Extension Manager menu option<br /> * The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br /> ** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br /> ** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br /> * Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br /> * To turn modules on or off, you can use the Module Settings page of the View-&gt;Application Settings dialog.<br /> <br /> <br /> *Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]<br /> <br /> '''Installation'''<br /> *Click on the cogwheel icon to start the extensions wizard (highlighted in red)<br /> [[image:Slicertoolbar.png|Extensions Wizard]]<br /> <br /> ===Listing of plug-ins===<br /> <br /> '''Available Extensions'''<br /> <br /> * [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''. Belongs to segmentation<br /> <br /> * [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''. Belongs to wizards<br /> <br /> * [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration, robust<br /> <br /> * [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust<br /> <br /> * [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust.<br /> <br /> * [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com) '''Not yet 3.6'''. Belongs to registration robust.<br /> <br /> * [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''. Belongs to tractography<br /> <br /> * [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)<br /> <br /> * [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to segmentation.<br /> <br /> * [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''. Belongs to registration robust.<br /> <br /> * [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''. Belongs to IGT.<br /> <br /> * [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''. Belongs to wizards.<br /> <br /> * [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''. Belongs to registration robust.<br /> <br /> * [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''. Belongs to DWI<br /> <br /> * [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to wizards<br /> <br /> * [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). Belongs to wizards<br /> <br /> * [[Image:Slicervmtk_logo.png|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)<br /> <br /> :*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins<br /> <br /> :*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models<br /> <br /> :*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface<br /> <br /> :*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution<br /> <br /> :*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures<br /> <br /> <br /> ====Example Extensions====<br /> <br /> * [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''<br /> <br /> * [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''<br /> <br /> * [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''<br /> <br /> * [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''<br /> <br /> * [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''<br /> <br /> <br /> <br /> '''Non-SPL Supported Compatibility Packages'''<br /> <br /> * [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''<br /> <br /> =QA=<br /> [[Slicer-3.6-QA|Slicer 3.6 QA table]]</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=13361 Modules:IA FEMesh-Documentation-3.6 2010-04-09T15:09:57Z <p>Vmagnotta: /* Source code &amp; documentation */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:IAFEmeshSlicer3Wizard.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[Image:IAFEMESHWithSpine.png|thumb|280px|User Interface with spine surface loaded]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|200px|IA-FEMesh Tabbed Wizard Interface]]<br /> | [[Image:IAFEMeshBlockEdit.png|thumb|200px|Block Editing Interface. From left to right: Edit, Split, Add, Delete, Combine, Mirror, Merge]]<br /> | [[Image:IAFEMeshQualityTab.png|thumb|200px|Mesh Quality Interface. Options include: Volume, Jacobian, Edge Collapse, Skew, Angle Out of Bounds]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *'''Common'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]<br /> <br /> *'''Filter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFaceHedgeHog.html vtkFaceHedgeHog]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityExtended.html vtkMeshQualityExtended]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAddUnstructuredHexahedronGridCell.html vtkMimxAddUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyImageBasedMaterialProperties.html vtkMimxApplyImageBasedMaterialProperties]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAttachBoundingBoxMesh.html vtkMimxAttachBoundingBoxMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromBounds.html vtkMimxBoundingBoxFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromUnstructuredGrid.html vtkMimxBoundingBoxFromUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSurfaceMesh.html vtkMimxBoundingBoxSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxToStructuredGrids.html vtkMimxBoundingBoxToStructuredGrids]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxClipImageFromBox.html vtkMimxClipImageFromBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxComputeNormalsFromPolydataFilter.html vtkMimxComputeNormalsFromPolydataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxConstrainedSmoothPolyDataFilter.html vtkMimxConstrainedSmoothPolyDataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCylindricalMesh.html vtkMimxCylindricalMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxDeleteUnstructuredHexahedronGridCell.html vtkMimxDeleteUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToPlanarStructuredGrid.html vtkMimxEdgeToPlanarStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToStructuredGrid.html vtkMimxEdgeToStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEditUnstructuredHexahedronGrid.html vtkMimxEditUnstructuredHexahedronGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEquivalancePoints.html vtkMimxEquivalancePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractElementNumbersOfaFaceFilter.html vtkMimxExtractElementNumbersOfaFaceFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridEdge.html vtkMimxExtractStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridFace.html vtkMimxExtractStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractSurface.html vtkMimxExtractSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtrudePolyData.html vtkMimxExtrudePolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFilterWin32Header.html vtkMimxFilterWin32Header]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFourPointsToStructuredPlanarMesh.html vtkMimxFourPointsToStructuredPlanarMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGenerateHexahedronMesh.html vtkMimxGenerateHexahedronMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGeometryFilter.html vtkMimxGeometryFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMapOriginalCellAndPointIds.html vtkMimxMapOriginalCellAndPointIds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergePoints.html vtkMimxMergePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMirrorUnstructuredHexahedronGridCell.html vtkMimxMirrorUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMorphStructuredGrid.html vtkMimxMorphStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPatchSurfaceMesh.html vtkMimxPatchSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarEllipticalInterpolation.html vtkMimxPlanarEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTransfiniteInterpolation.html vtkMimxPlanarTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTrilinearInterpolation.html vtkMimxPlanarTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataSingleSourceShortestPath.html vtkMimxPolyDataSingleSourceShortestPath]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRebinMaterialProperty.html vtkMimxRebinMaterialProperty]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodes.html vtkMimxRecalculateInteriorNodes]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodesTPS.html vtkMimxRecalculateInteriorNodesTPS]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectSurface.html vtkMimxSelectSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridEdge.html vtkMimxSetStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridFace.html vtkMimxSetStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSmoothUnstructuredGridFilter.html vtkMimxSmoothUnstructuredGridFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidEllipticalInterpolation.html vtkMimxSolidEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTransfiniteInterpolation.html vtkMimxSolidTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTrilinearInterpolation.html vtkMimxSolidTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSplitUnstructuredHexahedronGridCell.html vtkMimxSplitUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxStructuredPlanarToStructuredSolidGrid.html vtkMimxStructuredPlanarToStructuredSolidGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideBoundingBox.html vtkMimxSubdivideBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideCurve.html vtkMimxSubdivideCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromBoundingBox.html vtkMimxUnstructuredGridFromBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromFourPoints.html vtkMimxUnstructuredGridFromFourPoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredToStructuredGrid.html vtkMimxUnstructuredToStructuredGrid]<br /> <br /> *'''IO'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1itkMimxAbaqusMeshFileWriter.html itkMimxAbaqusMeshFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ReadHistogramBinValuesFilter.html itkMimxReadHistogramBinValuesFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> '''Adapter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ItkMeshToFEMMesh.html ItkMeshToFEMMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkPolyData.html itkMeshTovtkPolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkUnstructuredGrid.html itkMeshTovtkUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPolyDataToitkMesh.html vtkPolyDataToitkMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkUnstructuredGridToitkMesh.html vtkUnstructuredGridToitkMesh]<br /> <br /> *'''Widgets'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxWidget.html vtkMimxBoundingBoxWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBWidgetPlusIPWidget.html vtkMimxBWidgetPlusIPWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateBuildingBlockFromPickWidget.html vtkMimxCreateBuildingBlockFromPickWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateElementSetWidgetFEMesh.html vtkMimxCreateElementSetWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractCellWidget.html vtkMimxExtractCellWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractEdgeWidget.html vtkMimxExtractEdgeWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractFaceWidget.html vtkMimxExtractFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractMultipleFaceWidget.html vtkMimxExtractMultipleFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxModPointWidget.html vtkMimxModPointWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlaceLocalAxesWidget.html vtkMimxPlaceLocalAxesWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataWidget.html vtkMimxPolyDataWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidgetFEMesh.html vtkMimxSelectCellsWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidget.html vtkMimxSelectCellsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectPointsWidget.html vtkMimxSelectPointsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTraceContourWidget.html vtkMimxTraceContourWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridExtractWidget.html vtkMimxUnstructuredGridExtractWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridWidget.html vtkMimxUnstructuredGridWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxViewMergePointsWidget.html vtkMimxViewMergePointsWidget]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=13255 Documentation/3.6 2010-04-07T03:18:57Z <p>Vmagnotta: /* Listing of plug-ins */</p> <hr /> <div>This is work in progress<br /> <br /> =Main GUI=<br /> <br /> *[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)<br /> *[[Modules:EventBindings-3.6| &quot;Hot-keys&quot; and Keyboard Shortcuts]] (Wendy Plesniak)<br /> *[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br /> *[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br /> *[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)<br /> *[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)<br /> <br /> =Modules=<br /> *Please copy the template linked below, paste it into your page and customize it with your module's information.<br /> [[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]] <br /> *See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br /> *To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br /> <br /> Please adhere to the naming scheme for the module documentation:<br /> *[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br /> <br /> =Requirements for Modules=<br /> {| border=&quot;00&quot; cellpadding=&quot;5&quot; cellspacing=&quot;0&quot;<br /> |-<br /> | rowspan=&quot;2&quot;| <br /> * The module is '''feature complete''', it does everything that it advertises it can do<br /> * The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br /> * Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.<br /> *Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.<br /> * The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]<br /> ** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br /> ** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons. <br /> ** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)<br /> * Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.<br /> * Follow [[Documentation-3.5-Rons-Rules|&quot;Ron's rules for tools&quot;]]<br /> | style=&quot;background: #e5e5e5&quot; align=&quot;center&quot;| Examples for the Help and <br /> Acknowledgment Panels<br /> |-<br /> | style=&quot;background: #ebeced&quot;|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br /> |}<br /> <br /> =List of Modules added or significantly revised since the 3.4 release=<br /> * Interactive Editor<br /> * Volume Rendering<br /> * Colors (Nicole Aucoin)<br /> * MRI Bias Field Correction (Sylvain Jaume)<br /> * 4D Image (Viewer) (Junichi Tokuda)<br /> * 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)<br /> * Fast Marching segmentation (Andriy Fedorov)<br /> * Mesh Contour Segmentation]] (Peter Karasev)<br /> * Subvolume extraction with ROI widget (Andriy Fedorov)<br /> * Registration Metrics (HD and DSC) (Haytham Elhawary)<br /> * Measurements (rulers and angles) (Nicole Aucoin)<br /> * Affine registration (Casey Goodlett)<br /> * Collect Patient Fiducials (Andrew Wiles)<br /> * IGT Tool Selector (Andrew Wiles)<br /> * Fiducials (Nicole Aucoin)<br /> <br /> =List of pre-existing Modules=<br /> ==Core==<br /> *[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''<br /> *[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''<br /> *[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) <br /> **[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''<br /> *[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich) <br /> *[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin) <br /> *[[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) [[Modules:Measurements-Documentation-3.6 | '''3.6 in progress''']] <br /> *[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich) <br /> *[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''<br /> *[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin) <br /> *[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''<br /> *[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich) <br /> *[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''<br /> <br /> ==Specialized Modules==<br /> <br /> Please adhere to the naming scheme for the module documentation:<br /> *[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br /> <br /> ===Wizards===<br /> *[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)<br /> *[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta) '''3.6 In Progress'''<br /> <br /> ===Informatics Modules===<br /> *[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus) '''Not yet 3.6'''<br /> *[[Modules:QDECModule-Documentation-3.6| QDEC Module]] (Nicole Aucoin) <br /> *[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''<br /> <br /> ===Registration===<br /> *[[Slicer3:Registration|Overview of all Registration Modules ]] <br /> **[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett)<br /> **[[Modules:RegisterImagesMultiRes-Documentation-3.6|Register Images Robust Affine]] (Casey Goodlett)<br /> **[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Deformable B-Spline Registration]] (Bill Lorensen) '''in progress'''<br /> **[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial-Based Registration]] (Casey Goodlett)<br /> **[[Modules:Transforms-Documentation-3.6| Transforms Module for interactive rigid registration]] (Alex Yarmarkovich)<br /> **[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]] (Nicole Aucoin)<br /> **[[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''<br /> **[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''<br /> **[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''<br /> **[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br /> <br /> ===Segmentation===<br /> *Overview (Kilian)<br /> **[[Modules:EMSegment|EM Segment]] (Kilian Pohl) '''Not yet 3.6'''<br /> **[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Kilian Pohl) '''Not yet 3.6'''<br /> **[[Modules:EMSegment-Simple|EM Segment Simple]] (Kilian Pohl) '''Not yet 3.6'''<br /> **[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)<br /> **[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''<br /> **[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''<br /> <br /> ===Statistics===<br /> *[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''<br /> <br /> ===Diffusion===<br /> ====DWI====<br /> *Estimation<br /> **[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''<br /> *[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br /> *Filter<br /> **[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br /> **[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''<br /> **[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br /> *[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''<br /> *[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br /> <br /> ====DTI====<br /> *[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)<br /> *[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''<br /> *Analysis<br /> <br /> ====Tractography====<br /> *[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''<br /> *[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) <br /> *[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich) <br /> *[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''<br /> *[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''<br /> <br /> ===IGT===<br /> *[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''<br /> *[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''<br /> *[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''<br /> *[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''<br /> *[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles) '''Not yet 3.6'''<br /> <br /> <br /> ===Time Series===<br /> * [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''<br /> * [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''<br /> <br /> ===Filtering===<br /> *[[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)<br /> *[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''<br /> *[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''<br /> *[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich) <br /> *[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''<br /> *[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)<br /> *[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin) <br /> *Arithmetic<br /> **[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''<br /> **[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''<br /> ** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin) <br /> ** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''<br /> *Denoising<br /> **[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''<br /> **[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''<br /> **[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br /> **[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''<br /> *Morphology<br /> **[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''<br /> **[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''<br /> **[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''<br /> <br /> ===Surface Models===<br /> *[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin) <br /> *Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''<br /> *[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev) <br /> *[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br /> *[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br /> *[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br /> *[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich) <br /> *[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)<br /> <br /> ===Batch processing===<br /> *[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)<br /> *[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)<br /> *[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)<br /> *[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)<br /> <br /> ===Converters===<br /> *[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''<br /> *[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''<br /> *[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''<br /> *[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br /> *[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)<br /> <br /> =Slicer Extensions=<br /> <br /> ==Extensions for Downloading==<br /> ===Introduction===<br /> [[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]<br /> * Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.<br /> * Some of the extensions do not use the Slicer license. Please review carefully.<br /> * For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.<br /> * The version that is available through the extension manager is chosen by the developer of that extension <br /> <br /> We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.<br /> Click [http://www.nitrc.org/search/?type_of_search=soft&amp;words=slicer3&amp;Search.x=0&amp;Search.y=0&amp;Search=Search here] to see a listing of Slicer 3 extensions on NITRC.<br /> <br /> [[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br /> To add extension modules to an installed binary of slicer:<br /> * Use the View-&gt;Extension Manager menu option<br /> * The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br /> ** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br /> ** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br /> * Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br /> * To turn modules on or off, you can use the Module Settings page of the View-&gt;Application Settings dialog.<br /> <br /> <br /> *Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]<br /> <br /> '''Installation'''<br /> *Click on the icon to start the extensions wizard<br /> [[image:ExtensionsWizard.png|Extensions Wizard]]<br /> <br /> ===Listing of plug-ins===<br /> <br /> '''Available Extensions'''<br /> <br /> * [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''<br /> <br /> * [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''<br /> <br /> * [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Thorsten Rolfry '''Not yet 3.6'''<br /> <br /> * [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''<br /> <br /> * [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''<br /> <br /> * [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''<br /> <br /> * [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''<br /> <br /> * [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''<br /> <br /> * [[Modules:SpineSegmentation|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins, Daniel Haehn (haehn@bwh.harvard.edu)<br /> <br /> * [[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models, Daniel Haehn (haehn@bwh.harvard.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''<br /> <br /> * [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution, Daniel Haehn (haehn@bwh.harvard.edu) <br /> <br /> * [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures, Daniel Haehn (haehn@bwh.harvard.edu)<br /> <br /> <br /> ====Example Extensions====<br /> <br /> * [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''<br /> <br /> * [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''<br /> <br /> * [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''<br /> <br /> * [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''<br /> <br /> * [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''<br /> <br /> <br /> <br /> '''Deprecated Extensions'''<br /> <br /> * [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com) '''Not yet 3.6'''<br /> <br /> <br /> <br /> '''Non-SPL Supported Compatibility Packages'''<br /> <br /> * [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''</div> Vmagnotta https://www.slicer.org/w/index.php?title=Documentation/3.6&diff=13254 Documentation/3.6 2010-04-07T03:18:26Z <p>Vmagnotta: /* Wizards */</p> <hr /> <div>This is work in progress<br /> <br /> =Main GUI=<br /> <br /> *[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)<br /> *[[Modules:EventBindings-3.6| &quot;Hot-keys&quot; and Keyboard Shortcuts]] (Wendy Plesniak)<br /> *[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br /> *[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)<br /> *[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)<br /> *[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)<br /> <br /> =Modules=<br /> *Please copy the template linked below, paste it into your page and customize it with your module's information.<br /> [[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]] <br /> *See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs<br /> *To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]<br /> <br /> Please adhere to the naming scheme for the module documentation:<br /> *[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br /> <br /> =Requirements for Modules=<br /> {| border=&quot;00&quot; cellpadding=&quot;5&quot; cellspacing=&quot;0&quot;<br /> |-<br /> | rowspan=&quot;2&quot;| <br /> * The module is '''feature complete''', it does everything that it advertises it can do<br /> * The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br /> * Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.6#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.<br /> *Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.<br /> * The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]<br /> ** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.<br /> ** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons. <br /> ** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)<br /> * Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]]. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.<br /> * Follow [[Documentation-3.5-Rons-Rules|&quot;Ron's rules for tools&quot;]]<br /> | style=&quot;background: #e5e5e5&quot; align=&quot;center&quot;| Examples for the Help and <br /> Acknowledgment Panels<br /> |-<br /> | style=&quot;background: #ebeced&quot;|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]] <br /> |}<br /> <br /> =List of Modules added or significantly revised since the 3.4 release=<br /> * Interactive Editor<br /> * Volume Rendering<br /> * Colors (Nicole Aucoin)<br /> * MRI Bias Field Correction (Sylvain Jaume)<br /> * 4D Image (Viewer) (Junichi Tokuda)<br /> * 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)<br /> * Fast Marching segmentation (Andriy Fedorov)<br /> * Mesh Contour Segmentation]] (Peter Karasev)<br /> * Subvolume extraction with ROI widget (Andriy Fedorov)<br /> * Registration Metrics (HD and DSC) (Haytham Elhawary)<br /> * Measurements (rulers and angles) (Nicole Aucoin)<br /> * Affine registration (Casey Goodlett)<br /> * Collect Patient Fiducials (Andrew Wiles)<br /> * IGT Tool Selector (Andrew Wiles)<br /> * Fiducials (Nicole Aucoin)<br /> <br /> =List of pre-existing Modules=<br /> ==Core==<br /> *[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''<br /> *[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''<br /> *[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) <br /> **[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''<br /> *[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich) <br /> *[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin) <br /> *[[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) [[Modules:Measurements-Documentation-3.6 | '''3.6 in progress''']] <br /> *[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich) <br /> *[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''<br /> *[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin) <br /> *[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''<br /> *[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich) <br /> *[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''<br /> <br /> ==Specialized Modules==<br /> <br /> Please adhere to the naming scheme for the module documentation:<br /> *[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)<br /> <br /> ===Wizards===<br /> *[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)<br /> *[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta) '''3.6 In Progress'''<br /> <br /> ===Informatics Modules===<br /> *[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus) '''Not yet 3.6'''<br /> *[[Modules:QDECModule-Documentation-3.6| QDEC Module]] (Nicole Aucoin) <br /> *[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak) '''Not yet 3.6'''<br /> <br /> ===Registration===<br /> *[[Slicer3:Registration|Overview of all Registration Modules ]] <br /> **[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett)<br /> **[[Modules:RegisterImagesMultiRes-Documentation-3.6|Register Images Robust Affine]] (Casey Goodlett)<br /> **[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Deformable B-Spline Registration]] (Bill Lorensen) '''in progress'''<br /> **[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial-Based Registration]] (Casey Goodlett)<br /> **[[Modules:Transforms-Documentation-3.6| Transforms Module for interactive rigid registration]] (Alex Yarmarkovich)<br /> **[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]] (Nicole Aucoin)<br /> **[[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary) '''Not yet 3.6'''<br /> **[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''<br /> **[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''<br /> **[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br /> <br /> ===Segmentation===<br /> *Overview (Kilian)<br /> **[[Modules:EMSegment|EM Segment]] (Kilian Pohl) '''Not yet 3.6'''<br /> **[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Kilian Pohl) '''Not yet 3.6'''<br /> **[[Modules:EMSegment-Simple|EM Segment Simple]] (Kilian Pohl) '''Not yet 3.6'''<br /> **[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)<br /> **[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''<br /> **[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''<br /> <br /> ===Statistics===<br /> *[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''<br /> <br /> ===Diffusion===<br /> ====DWI====<br /> *Estimation<br /> **[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''<br /> *[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br /> *Filter<br /> **[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br /> **[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''<br /> **[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''<br /> *[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''<br /> *[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''<br /> <br /> ====DTI====<br /> *[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)<br /> *[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''<br /> *Analysis<br /> <br /> ====Tractography====<br /> *[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar) '''Not yet 3.6'''<br /> *[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) <br /> *[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich) <br /> *[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''<br /> *[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''<br /> <br /> ===IGT===<br /> *[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda) '''Not yet 3.6'''<br /> *[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''<br /> *[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''<br /> *[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''<br /> *[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles) '''Not yet 3.6'''<br /> <br /> <br /> ===Time Series===<br /> * [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''<br /> * [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda) '''Not yet 3.6'''<br /> <br /> ===Filtering===<br /> *[[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)<br /> *[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''<br /> *[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''<br /> *[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich) <br /> *[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''<br /> *[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)<br /> *[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin) <br /> *Arithmetic<br /> **[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''<br /> **[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen) '''Not yet 3.6'''<br /> ** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin) <br /> ** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''<br /> *Denoising<br /> **[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]] (Bill Lorensen checked this in) '''Not yet 3.6'''<br /> **[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''<br /> **[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) '''Not yet 3.6'''<br /> **[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen) '''Not yet 3.6'''<br /> *Morphology<br /> **[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen) '''Not yet 3.6'''<br /> **[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''<br /> **[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen) '''Not yet 3.6'''<br /> <br /> ===Surface Models===<br /> *[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin) <br /> *Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''<br /> *[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev) <br /> *[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br /> *[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br /> *[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br /> *[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich) <br /> *[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)<br /> <br /> ===Batch processing===<br /> *[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)<br /> *[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)<br /> *[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)<br /> *[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)<br /> <br /> ===Converters===<br /> *[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen) '''Not yet 3.6'''<br /> *[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao) '''Not yet 3.6'''<br /> *[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen) '''Not yet 3.6'''<br /> *[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''<br /> *[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)<br /> <br /> =Slicer Extensions=<br /> <br /> ==Extensions for Downloading==<br /> ===Introduction===<br /> [[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]<br /> * Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.<br /> * Some of the extensions do not use the Slicer license. Please review carefully.<br /> * For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.<br /> * The version that is available through the extension manager is chosen by the developer of that extension <br /> <br /> We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.<br /> Click [http://www.nitrc.org/search/?type_of_search=soft&amp;words=slicer3&amp;Search.x=0&amp;Search.y=0&amp;Search=Search here] to see a listing of Slicer 3 extensions on NITRC.<br /> <br /> [[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]<br /> To add extension modules to an installed binary of slicer:<br /> * Use the View-&gt;Extension Manager menu option<br /> * The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.<br /> ** '''Note''' installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.<br /> ** You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).<br /> * Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.<br /> * To turn modules on or off, you can use the Module Settings page of the View-&gt;Application Settings dialog.<br /> <br /> <br /> *Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]<br /> <br /> '''Installation'''<br /> *Click on the icon to start the extensions wizard<br /> [[image:ExtensionsWizard.png|Extensions Wizard]]<br /> <br /> ===Listing of plug-ins===<br /> <br /> '''Available Extensions'''<br /> <br /> * [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''<br /> <br /> * [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''<br /> <br /> * [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Thorsten Rolfry '''Not yet 3.6'''<br /> <br /> * [[Modules:DiffusionWarp|DiffusionWarp]] '''Not yet 3.6'''<br /> <br /> * [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''<br /> <br /> * [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''<br /> <br /> * [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''<br /> <br /> * [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''<br /> <br /> * [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''<br /> <br /> * [[Modules:SpineSegmentation|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins, Daniel Haehn (haehn@bwh.harvard.edu)<br /> <br /> * [[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models, Daniel Haehn (haehn@bwh.harvard.edu) '''Not yet 3.6'''<br /> <br /> * [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface '''Not yet 3.6'''<br /> <br /> * [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution, Daniel Haehn (haehn@bwh.harvard.edu) <br /> <br /> * [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures, Daniel Haehn (haehn@bwh.harvard.edu)<br /> <br /> <br /> ====Example Extensions====<br /> <br /> * [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''<br /> <br /> * [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''<br /> <br /> * [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''<br /> <br /> * [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''<br /> <br /> * [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''<br /> <br /> <br /> <br /> '''Deprecated Extensions'''<br /> <br /> * [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com) '''Not yet 3.6'''<br /> <br /> <br /> <br /> '''Non-SPL Supported Compatibility Packages'''<br /> <br /> * [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=13040 Modules:IA FEMesh-Documentation-3.6 2010-04-01T20:49:53Z <p>Vmagnotta: /* Quick Tour of Features and Use */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:IAFEmeshSlicer3Wizard.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[Image:IAFEMESHWithSpine.png|thumb|280px|User Interface with spine surface loaded]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|200px|IA-FEMesh Tabbed Wizard Interface]]<br /> | [[Image:IAFEMeshBlockEdit.png|thumb|200px|Block Editing Interface. From left to right: Edit, Split, Add, Delete, Combine, Mirror, Merge]]<br /> | [[Image:IAFEMeshQualityTab.png|thumb|200px|Mesh Quality Interface. Options include: Volume, Jacobian, Edge Collapse, Skew, Angle Out of Bounds]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *'''Common'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]<br /> <br /> *'''Filter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFaceHedgeHog.html vtkFaceHedgeHog]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityExtended.html vtkMeshQualityExtended]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAddUnstructuredHexahedronGridCell.html vtkMimxAddUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyImageBasedMaterialProperties.html vtkMimxApplyImageBasedMaterialProperties]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAttachBoundingBoxMesh.html vtkMimxAttachBoundingBoxMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromBounds.html vtkMimxBoundingBoxFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromUnstructuredGrid.html vtkMimxBoundingBoxFromUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSurfaceMesh.html vtkMimxBoundingBoxSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxToStructuredGrids.html vtkMimxBoundingBoxToStructuredGrids]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxButterflyMeshFromBounds.html vtkMimxButterflyMeshFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxClipImageFromBox.html vtkMimxClipImageFromBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxComputeNormalsFromPolydataFilter.html vtkMimxComputeNormalsFromPolydataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxConstrainedSmoothPolyDataFilter.html vtkMimxConstrainedSmoothPolyDataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCylindricalMesh.html vtkMimxCylindricalMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxDeleteUnstructuredHexahedronGridCell.html vtkMimxDeleteUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToPlanarStructuredGrid.html vtkMimxEdgeToPlanarStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToStructuredGrid.html vtkMimxEdgeToStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEditUnstructuredHexahedronGrid.html vtkMimxEditUnstructuredHexahedronGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEquivalancePoints.html vtkMimxEquivalancePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractElementNumbersOfaFaceFilter.html vtkMimxExtractElementNumbersOfaFaceFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridEdge.html vtkMimxExtractStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridFace.html vtkMimxExtractStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractSurface.html vtkMimxExtractSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtrudePolyData.html vtkMimxExtrudePolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFilterWin32Header.html vtkMimxFilterWin32Header]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFourPointsToStructuredPlanarMesh.html vtkMimxFourPointsToStructuredPlanarMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGenerateHexahedronMesh.html vtkMimxGenerateHexahedronMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGeometryFilter.html vtkMimxGeometryFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMapOriginalCellAndPointIds.html vtkMimxMapOriginalCellAndPointIds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergePoints.html vtkMimxMergePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMirrorUnstructuredHexahedronGridCell.html vtkMimxMirrorUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMorphStructuredGrid.html vtkMimxMorphStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPatchSurfaceMesh.html vtkMimxPatchSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarEllipticalInterpolation.html vtkMimxPlanarEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTransfiniteInterpolation.html vtkMimxPlanarTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTrilinearInterpolation.html vtkMimxPlanarTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataSingleSourceShortestPath.html vtkMimxPolyDataSingleSourceShortestPath]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRebinMaterialProperty.html vtkMimxRebinMaterialProperty]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodes.html vtkMimxRecalculateInteriorNodes]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodesTPS.html vtkMimxRecalculateInteriorNodesTPS]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectSurface.html vtkMimxSelectSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridEdge.html vtkMimxSetStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridFace.html vtkMimxSetStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSmoothUnstructuredGridFilter.html vtkMimxSmoothUnstructuredGridFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidEllipticalInterpolation.html vtkMimxSolidEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTransfiniteInterpolation.html vtkMimxSolidTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTrilinearInterpolation.html vtkMimxSolidTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSplitUnstructuredHexahedronGridCell.html vtkMimxSplitUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxStructuredPlanarToStructuredSolidGrid.html vtkMimxStructuredPlanarToStructuredSolidGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideBoundingBox.html vtkMimxSubdivideBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideCurve.html vtkMimxSubdivideCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromBoundingBox.html vtkMimxUnstructuredGridFromBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromFourPoints.html vtkMimxUnstructuredGridFromFourPoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredToStructuredGrid.html vtkMimxUnstructuredToStructuredGrid]<br /> <br /> *'''IO'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1itkMimxAbaqusMeshFileWriter.html itkMimxAbaqusMeshFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ReadHistogramBinValuesFilter.html itkMimxReadHistogramBinValuesFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> '''Adapter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ItkMeshToFEMMesh.html ItkMeshToFEMMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkPolyData.html itkMeshTovtkPolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkUnstructuredGrid.html itkMeshTovtkUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPolyDataToitkMesh.html vtkPolyDataToitkMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkUnstructuredGridToitkMesh.html vtkUnstructuredGridToitkMesh]<br /> <br /> *'''Widgets'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxWidget.html vtkMimxBoundingBoxWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBWidgetPlusIPWidget.html vtkMimxBWidgetPlusIPWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateBuildingBlockFromPickWidget.html vtkMimxCreateBuildingBlockFromPickWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateElementSetWidgetFEMesh.html vtkMimxCreateElementSetWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractCellWidget.html vtkMimxExtractCellWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractEdgeWidget.html vtkMimxExtractEdgeWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractFaceWidget.html vtkMimxExtractFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractMultipleFaceWidget.html vtkMimxExtractMultipleFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxModPointWidget.html vtkMimxModPointWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlaceLocalAxesWidget.html vtkMimxPlaceLocalAxesWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataWidget.html vtkMimxPolyDataWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidgetFEMesh.html vtkMimxSelectCellsWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidget.html vtkMimxSelectCellsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectPointsWidget.html vtkMimxSelectPointsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTraceContourWidget.html vtkMimxTraceContourWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridExtractWidget.html vtkMimxUnstructuredGridExtractWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridWidget.html vtkMimxUnstructuredGridWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxViewMergePointsWidget.html vtkMimxViewMergePointsWidget]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=13039 Modules:IA FEMesh-Documentation-3.6 2010-04-01T20:49:28Z <p>Vmagnotta: /* Quick Tour of Features and Use */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:IAFEmeshSlicer3Wizard.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[Image:IAFEMESHWithSpine.png|thumb|280px|User Interface with spine surface loaded]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|200px|IA-FEMesh Tabbed Wizard Interface]]<br /> [[Image:IAFEMeshBlockEdit.png|thumb|200px|Block Editing Interface. From left to right: Edit, Split, Add, Delete, Combine, Mirror, Merge]]<br /> [[Image:IAFEMeshQualityTab.png|thumb|200px|Mesh Quality Interface. Options include: Volume, Jacobian, Edge Collapse, Skew, Angle Out of Bounds]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *'''Common'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]<br /> <br /> *'''Filter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFaceHedgeHog.html vtkFaceHedgeHog]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityExtended.html vtkMeshQualityExtended]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAddUnstructuredHexahedronGridCell.html vtkMimxAddUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyImageBasedMaterialProperties.html vtkMimxApplyImageBasedMaterialProperties]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAttachBoundingBoxMesh.html vtkMimxAttachBoundingBoxMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromBounds.html vtkMimxBoundingBoxFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromUnstructuredGrid.html vtkMimxBoundingBoxFromUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSurfaceMesh.html vtkMimxBoundingBoxSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxToStructuredGrids.html vtkMimxBoundingBoxToStructuredGrids]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxButterflyMeshFromBounds.html vtkMimxButterflyMeshFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxClipImageFromBox.html vtkMimxClipImageFromBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxComputeNormalsFromPolydataFilter.html vtkMimxComputeNormalsFromPolydataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxConstrainedSmoothPolyDataFilter.html vtkMimxConstrainedSmoothPolyDataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCylindricalMesh.html vtkMimxCylindricalMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxDeleteUnstructuredHexahedronGridCell.html vtkMimxDeleteUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToPlanarStructuredGrid.html vtkMimxEdgeToPlanarStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToStructuredGrid.html vtkMimxEdgeToStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEditUnstructuredHexahedronGrid.html vtkMimxEditUnstructuredHexahedronGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEquivalancePoints.html vtkMimxEquivalancePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractElementNumbersOfaFaceFilter.html vtkMimxExtractElementNumbersOfaFaceFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridEdge.html vtkMimxExtractStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridFace.html vtkMimxExtractStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractSurface.html vtkMimxExtractSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtrudePolyData.html vtkMimxExtrudePolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFilterWin32Header.html vtkMimxFilterWin32Header]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFourPointsToStructuredPlanarMesh.html vtkMimxFourPointsToStructuredPlanarMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGenerateHexahedronMesh.html vtkMimxGenerateHexahedronMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGeometryFilter.html vtkMimxGeometryFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMapOriginalCellAndPointIds.html vtkMimxMapOriginalCellAndPointIds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergePoints.html vtkMimxMergePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMirrorUnstructuredHexahedronGridCell.html vtkMimxMirrorUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMorphStructuredGrid.html vtkMimxMorphStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPatchSurfaceMesh.html vtkMimxPatchSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarEllipticalInterpolation.html vtkMimxPlanarEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTransfiniteInterpolation.html vtkMimxPlanarTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTrilinearInterpolation.html vtkMimxPlanarTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataSingleSourceShortestPath.html vtkMimxPolyDataSingleSourceShortestPath]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRebinMaterialProperty.html vtkMimxRebinMaterialProperty]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodes.html vtkMimxRecalculateInteriorNodes]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodesTPS.html vtkMimxRecalculateInteriorNodesTPS]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectSurface.html vtkMimxSelectSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridEdge.html vtkMimxSetStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridFace.html vtkMimxSetStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSmoothUnstructuredGridFilter.html vtkMimxSmoothUnstructuredGridFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidEllipticalInterpolation.html vtkMimxSolidEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTransfiniteInterpolation.html vtkMimxSolidTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTrilinearInterpolation.html vtkMimxSolidTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSplitUnstructuredHexahedronGridCell.html vtkMimxSplitUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxStructuredPlanarToStructuredSolidGrid.html vtkMimxStructuredPlanarToStructuredSolidGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideBoundingBox.html vtkMimxSubdivideBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideCurve.html vtkMimxSubdivideCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromBoundingBox.html vtkMimxUnstructuredGridFromBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromFourPoints.html vtkMimxUnstructuredGridFromFourPoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredToStructuredGrid.html vtkMimxUnstructuredToStructuredGrid]<br /> <br /> *'''IO'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1itkMimxAbaqusMeshFileWriter.html itkMimxAbaqusMeshFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ReadHistogramBinValuesFilter.html itkMimxReadHistogramBinValuesFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> '''Adapter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ItkMeshToFEMMesh.html ItkMeshToFEMMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkPolyData.html itkMeshTovtkPolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkUnstructuredGrid.html itkMeshTovtkUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPolyDataToitkMesh.html vtkPolyDataToitkMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkUnstructuredGridToitkMesh.html vtkUnstructuredGridToitkMesh]<br /> <br /> *'''Widgets'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxWidget.html vtkMimxBoundingBoxWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBWidgetPlusIPWidget.html vtkMimxBWidgetPlusIPWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateBuildingBlockFromPickWidget.html vtkMimxCreateBuildingBlockFromPickWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateElementSetWidgetFEMesh.html vtkMimxCreateElementSetWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractCellWidget.html vtkMimxExtractCellWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractEdgeWidget.html vtkMimxExtractEdgeWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractFaceWidget.html vtkMimxExtractFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractMultipleFaceWidget.html vtkMimxExtractMultipleFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxModPointWidget.html vtkMimxModPointWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlaceLocalAxesWidget.html vtkMimxPlaceLocalAxesWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataWidget.html vtkMimxPolyDataWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidgetFEMesh.html vtkMimxSelectCellsWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidget.html vtkMimxSelectCellsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectPointsWidget.html vtkMimxSelectPointsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTraceContourWidget.html vtkMimxTraceContourWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridExtractWidget.html vtkMimxUnstructuredGridExtractWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridWidget.html vtkMimxUnstructuredGridWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxViewMergePointsWidget.html vtkMimxViewMergePointsWidget]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=13038 Modules:IA FEMesh-Documentation-3.6 2010-04-01T20:46:59Z <p>Vmagnotta: /* Quick Tour of Features and Use */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:IAFEmeshSlicer3Wizard.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[Image:IAFEMESHWithSpine.png|thumb|280px|User Interface with spine surface loaded]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|200px|IA-FEMesh Tabbed Wizard Interface]]<br /> [[Image:IAFEMeshBlockEdit.png|thumb|200px|Block Editing Interface]]<br /> [[Image:IAFEMeshQualityTab.png|thumb|200px|Mesh Quality Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *'''Common'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]<br /> <br /> *'''Filter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFaceHedgeHog.html vtkFaceHedgeHog]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityExtended.html vtkMeshQualityExtended]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAddUnstructuredHexahedronGridCell.html vtkMimxAddUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyImageBasedMaterialProperties.html vtkMimxApplyImageBasedMaterialProperties]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAttachBoundingBoxMesh.html vtkMimxAttachBoundingBoxMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromBounds.html vtkMimxBoundingBoxFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromUnstructuredGrid.html vtkMimxBoundingBoxFromUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSurfaceMesh.html vtkMimxBoundingBoxSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxToStructuredGrids.html vtkMimxBoundingBoxToStructuredGrids]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxButterflyMeshFromBounds.html vtkMimxButterflyMeshFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxClipImageFromBox.html vtkMimxClipImageFromBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxComputeNormalsFromPolydataFilter.html vtkMimxComputeNormalsFromPolydataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxConstrainedSmoothPolyDataFilter.html vtkMimxConstrainedSmoothPolyDataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCylindricalMesh.html vtkMimxCylindricalMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxDeleteUnstructuredHexahedronGridCell.html vtkMimxDeleteUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToPlanarStructuredGrid.html vtkMimxEdgeToPlanarStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToStructuredGrid.html vtkMimxEdgeToStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEditUnstructuredHexahedronGrid.html vtkMimxEditUnstructuredHexahedronGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEquivalancePoints.html vtkMimxEquivalancePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractElementNumbersOfaFaceFilter.html vtkMimxExtractElementNumbersOfaFaceFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridEdge.html vtkMimxExtractStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridFace.html vtkMimxExtractStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractSurface.html vtkMimxExtractSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtrudePolyData.html vtkMimxExtrudePolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFilterWin32Header.html vtkMimxFilterWin32Header]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFourPointsToStructuredPlanarMesh.html vtkMimxFourPointsToStructuredPlanarMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGenerateHexahedronMesh.html vtkMimxGenerateHexahedronMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGeometryFilter.html vtkMimxGeometryFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMapOriginalCellAndPointIds.html vtkMimxMapOriginalCellAndPointIds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergePoints.html vtkMimxMergePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMirrorUnstructuredHexahedronGridCell.html vtkMimxMirrorUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMorphStructuredGrid.html vtkMimxMorphStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPatchSurfaceMesh.html vtkMimxPatchSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarEllipticalInterpolation.html vtkMimxPlanarEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTransfiniteInterpolation.html vtkMimxPlanarTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTrilinearInterpolation.html vtkMimxPlanarTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataSingleSourceShortestPath.html vtkMimxPolyDataSingleSourceShortestPath]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRebinMaterialProperty.html vtkMimxRebinMaterialProperty]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodes.html vtkMimxRecalculateInteriorNodes]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodesTPS.html vtkMimxRecalculateInteriorNodesTPS]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectSurface.html vtkMimxSelectSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridEdge.html vtkMimxSetStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridFace.html vtkMimxSetStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSmoothUnstructuredGridFilter.html vtkMimxSmoothUnstructuredGridFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidEllipticalInterpolation.html vtkMimxSolidEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTransfiniteInterpolation.html vtkMimxSolidTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTrilinearInterpolation.html vtkMimxSolidTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSplitUnstructuredHexahedronGridCell.html vtkMimxSplitUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxStructuredPlanarToStructuredSolidGrid.html vtkMimxStructuredPlanarToStructuredSolidGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideBoundingBox.html vtkMimxSubdivideBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideCurve.html vtkMimxSubdivideCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromBoundingBox.html vtkMimxUnstructuredGridFromBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromFourPoints.html vtkMimxUnstructuredGridFromFourPoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredToStructuredGrid.html vtkMimxUnstructuredToStructuredGrid]<br /> <br /> *'''IO'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1itkMimxAbaqusMeshFileWriter.html itkMimxAbaqusMeshFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ReadHistogramBinValuesFilter.html itkMimxReadHistogramBinValuesFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> '''Adapter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ItkMeshToFEMMesh.html ItkMeshToFEMMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkPolyData.html itkMeshTovtkPolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkUnstructuredGrid.html itkMeshTovtkUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPolyDataToitkMesh.html vtkPolyDataToitkMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkUnstructuredGridToitkMesh.html vtkUnstructuredGridToitkMesh]<br /> <br /> *'''Widgets'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxWidget.html vtkMimxBoundingBoxWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBWidgetPlusIPWidget.html vtkMimxBWidgetPlusIPWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateBuildingBlockFromPickWidget.html vtkMimxCreateBuildingBlockFromPickWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateElementSetWidgetFEMesh.html vtkMimxCreateElementSetWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractCellWidget.html vtkMimxExtractCellWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractEdgeWidget.html vtkMimxExtractEdgeWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractFaceWidget.html vtkMimxExtractFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractMultipleFaceWidget.html vtkMimxExtractMultipleFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxModPointWidget.html vtkMimxModPointWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlaceLocalAxesWidget.html vtkMimxPlaceLocalAxesWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataWidget.html vtkMimxPolyDataWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidgetFEMesh.html vtkMimxSelectCellsWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidget.html vtkMimxSelectCellsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectPointsWidget.html vtkMimxSelectPointsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTraceContourWidget.html vtkMimxTraceContourWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridExtractWidget.html vtkMimxUnstructuredGridExtractWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridWidget.html vtkMimxUnstructuredGridWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxViewMergePointsWidget.html vtkMimxViewMergePointsWidget]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=13037 Modules:IA FEMesh-Documentation-3.6 2010-04-01T20:45:52Z <p>Vmagnotta: /* Quick Tour of Features and Use */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:IAFEmeshSlicer3Wizard.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[Image:IAFEMESHWithSpine.png|thumb|280px|User Interface with spine surface loaded]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|200px|IA-FEMesh Tabbed Wizard Interface]]<br /> [[Image:IAFEMeshBlockEdit.png|thumb|200px|IA-FEMesh Tabbed Wizard Interface]]<br /> [[Image:IAFEMeshQualityTab.png|thumb|200px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *'''Common'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]<br /> <br /> *'''Filter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFaceHedgeHog.html vtkFaceHedgeHog]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityExtended.html vtkMeshQualityExtended]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAddUnstructuredHexahedronGridCell.html vtkMimxAddUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyImageBasedMaterialProperties.html vtkMimxApplyImageBasedMaterialProperties]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAttachBoundingBoxMesh.html vtkMimxAttachBoundingBoxMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromBounds.html vtkMimxBoundingBoxFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromUnstructuredGrid.html vtkMimxBoundingBoxFromUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSurfaceMesh.html vtkMimxBoundingBoxSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxToStructuredGrids.html vtkMimxBoundingBoxToStructuredGrids]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxButterflyMeshFromBounds.html vtkMimxButterflyMeshFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxClipImageFromBox.html vtkMimxClipImageFromBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxComputeNormalsFromPolydataFilter.html vtkMimxComputeNormalsFromPolydataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxConstrainedSmoothPolyDataFilter.html vtkMimxConstrainedSmoothPolyDataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCylindricalMesh.html vtkMimxCylindricalMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxDeleteUnstructuredHexahedronGridCell.html vtkMimxDeleteUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToPlanarStructuredGrid.html vtkMimxEdgeToPlanarStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToStructuredGrid.html vtkMimxEdgeToStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEditUnstructuredHexahedronGrid.html vtkMimxEditUnstructuredHexahedronGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEquivalancePoints.html vtkMimxEquivalancePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractElementNumbersOfaFaceFilter.html vtkMimxExtractElementNumbersOfaFaceFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridEdge.html vtkMimxExtractStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridFace.html vtkMimxExtractStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractSurface.html vtkMimxExtractSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtrudePolyData.html vtkMimxExtrudePolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFilterWin32Header.html vtkMimxFilterWin32Header]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFourPointsToStructuredPlanarMesh.html vtkMimxFourPointsToStructuredPlanarMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGenerateHexahedronMesh.html vtkMimxGenerateHexahedronMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGeometryFilter.html vtkMimxGeometryFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMapOriginalCellAndPointIds.html vtkMimxMapOriginalCellAndPointIds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergePoints.html vtkMimxMergePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMirrorUnstructuredHexahedronGridCell.html vtkMimxMirrorUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMorphStructuredGrid.html vtkMimxMorphStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPatchSurfaceMesh.html vtkMimxPatchSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarEllipticalInterpolation.html vtkMimxPlanarEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTransfiniteInterpolation.html vtkMimxPlanarTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTrilinearInterpolation.html vtkMimxPlanarTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataSingleSourceShortestPath.html vtkMimxPolyDataSingleSourceShortestPath]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRebinMaterialProperty.html vtkMimxRebinMaterialProperty]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodes.html vtkMimxRecalculateInteriorNodes]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodesTPS.html vtkMimxRecalculateInteriorNodesTPS]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectSurface.html vtkMimxSelectSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridEdge.html vtkMimxSetStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridFace.html vtkMimxSetStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSmoothUnstructuredGridFilter.html vtkMimxSmoothUnstructuredGridFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidEllipticalInterpolation.html vtkMimxSolidEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTransfiniteInterpolation.html vtkMimxSolidTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTrilinearInterpolation.html vtkMimxSolidTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSplitUnstructuredHexahedronGridCell.html vtkMimxSplitUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxStructuredPlanarToStructuredSolidGrid.html vtkMimxStructuredPlanarToStructuredSolidGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideBoundingBox.html vtkMimxSubdivideBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideCurve.html vtkMimxSubdivideCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromBoundingBox.html vtkMimxUnstructuredGridFromBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromFourPoints.html vtkMimxUnstructuredGridFromFourPoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredToStructuredGrid.html vtkMimxUnstructuredToStructuredGrid]<br /> <br /> *'''IO'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1itkMimxAbaqusMeshFileWriter.html itkMimxAbaqusMeshFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ReadHistogramBinValuesFilter.html itkMimxReadHistogramBinValuesFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> '''Adapter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ItkMeshToFEMMesh.html ItkMeshToFEMMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkPolyData.html itkMeshTovtkPolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkUnstructuredGrid.html itkMeshTovtkUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPolyDataToitkMesh.html vtkPolyDataToitkMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkUnstructuredGridToitkMesh.html vtkUnstructuredGridToitkMesh]<br /> <br /> *'''Widgets'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxWidget.html vtkMimxBoundingBoxWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBWidgetPlusIPWidget.html vtkMimxBWidgetPlusIPWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateBuildingBlockFromPickWidget.html vtkMimxCreateBuildingBlockFromPickWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateElementSetWidgetFEMesh.html vtkMimxCreateElementSetWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractCellWidget.html vtkMimxExtractCellWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractEdgeWidget.html vtkMimxExtractEdgeWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractFaceWidget.html vtkMimxExtractFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractMultipleFaceWidget.html vtkMimxExtractMultipleFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxModPointWidget.html vtkMimxModPointWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlaceLocalAxesWidget.html vtkMimxPlaceLocalAxesWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataWidget.html vtkMimxPolyDataWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidgetFEMesh.html vtkMimxSelectCellsWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidget.html vtkMimxSelectCellsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectPointsWidget.html vtkMimxSelectPointsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTraceContourWidget.html vtkMimxTraceContourWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridExtractWidget.html vtkMimxUnstructuredGridExtractWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridWidget.html vtkMimxUnstructuredGridWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxViewMergePointsWidget.html vtkMimxViewMergePointsWidget]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=File:IAFEMeshQualityTab.png&diff=13036 File:IAFEMeshQualityTab.png 2010-04-01T20:44:49Z <p>Vmagnotta: </p> <hr /> <div></div> Vmagnotta https://www.slicer.org/w/index.php?title=File:IAFEMeshBlockEdit.png&diff=13035 File:IAFEMeshBlockEdit.png 2010-04-01T20:44:20Z <p>Vmagnotta: </p> <hr /> <div></div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=13034 Modules:IA FEMesh-Documentation-3.6 2010-04-01T20:40:29Z <p>Vmagnotta: /* IA_FEMesh */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:IAFEmeshSlicer3Wizard.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[Image:IAFEMESHWithSpine.png|thumb|280px|User Interface with spine surface loaded]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *'''Common'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]<br /> <br /> *'''Filter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFaceHedgeHog.html vtkFaceHedgeHog]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityExtended.html vtkMeshQualityExtended]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAddUnstructuredHexahedronGridCell.html vtkMimxAddUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyImageBasedMaterialProperties.html vtkMimxApplyImageBasedMaterialProperties]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAttachBoundingBoxMesh.html vtkMimxAttachBoundingBoxMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromBounds.html vtkMimxBoundingBoxFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromUnstructuredGrid.html vtkMimxBoundingBoxFromUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSurfaceMesh.html vtkMimxBoundingBoxSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxToStructuredGrids.html vtkMimxBoundingBoxToStructuredGrids]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxButterflyMeshFromBounds.html vtkMimxButterflyMeshFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxClipImageFromBox.html vtkMimxClipImageFromBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxComputeNormalsFromPolydataFilter.html vtkMimxComputeNormalsFromPolydataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxConstrainedSmoothPolyDataFilter.html vtkMimxConstrainedSmoothPolyDataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCylindricalMesh.html vtkMimxCylindricalMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxDeleteUnstructuredHexahedronGridCell.html vtkMimxDeleteUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToPlanarStructuredGrid.html vtkMimxEdgeToPlanarStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToStructuredGrid.html vtkMimxEdgeToStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEditUnstructuredHexahedronGrid.html vtkMimxEditUnstructuredHexahedronGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEquivalancePoints.html vtkMimxEquivalancePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractElementNumbersOfaFaceFilter.html vtkMimxExtractElementNumbersOfaFaceFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridEdge.html vtkMimxExtractStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridFace.html vtkMimxExtractStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractSurface.html vtkMimxExtractSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtrudePolyData.html vtkMimxExtrudePolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFilterWin32Header.html vtkMimxFilterWin32Header]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFourPointsToStructuredPlanarMesh.html vtkMimxFourPointsToStructuredPlanarMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGenerateHexahedronMesh.html vtkMimxGenerateHexahedronMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGeometryFilter.html vtkMimxGeometryFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMapOriginalCellAndPointIds.html vtkMimxMapOriginalCellAndPointIds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergePoints.html vtkMimxMergePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMirrorUnstructuredHexahedronGridCell.html vtkMimxMirrorUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMorphStructuredGrid.html vtkMimxMorphStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPatchSurfaceMesh.html vtkMimxPatchSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarEllipticalInterpolation.html vtkMimxPlanarEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTransfiniteInterpolation.html vtkMimxPlanarTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTrilinearInterpolation.html vtkMimxPlanarTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataSingleSourceShortestPath.html vtkMimxPolyDataSingleSourceShortestPath]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRebinMaterialProperty.html vtkMimxRebinMaterialProperty]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodes.html vtkMimxRecalculateInteriorNodes]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodesTPS.html vtkMimxRecalculateInteriorNodesTPS]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectSurface.html vtkMimxSelectSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridEdge.html vtkMimxSetStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridFace.html vtkMimxSetStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSmoothUnstructuredGridFilter.html vtkMimxSmoothUnstructuredGridFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidEllipticalInterpolation.html vtkMimxSolidEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTransfiniteInterpolation.html vtkMimxSolidTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTrilinearInterpolation.html vtkMimxSolidTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSplitUnstructuredHexahedronGridCell.html vtkMimxSplitUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxStructuredPlanarToStructuredSolidGrid.html vtkMimxStructuredPlanarToStructuredSolidGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideBoundingBox.html vtkMimxSubdivideBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideCurve.html vtkMimxSubdivideCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromBoundingBox.html vtkMimxUnstructuredGridFromBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromFourPoints.html vtkMimxUnstructuredGridFromFourPoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredToStructuredGrid.html vtkMimxUnstructuredToStructuredGrid]<br /> <br /> *'''IO'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1itkMimxAbaqusMeshFileWriter.html itkMimxAbaqusMeshFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ReadHistogramBinValuesFilter.html itkMimxReadHistogramBinValuesFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> '''Adapter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ItkMeshToFEMMesh.html ItkMeshToFEMMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkPolyData.html itkMeshTovtkPolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkUnstructuredGrid.html itkMeshTovtkUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPolyDataToitkMesh.html vtkPolyDataToitkMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkUnstructuredGridToitkMesh.html vtkUnstructuredGridToitkMesh]<br /> <br /> *'''Widgets'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxWidget.html vtkMimxBoundingBoxWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBWidgetPlusIPWidget.html vtkMimxBWidgetPlusIPWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateBuildingBlockFromPickWidget.html vtkMimxCreateBuildingBlockFromPickWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateElementSetWidgetFEMesh.html vtkMimxCreateElementSetWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractCellWidget.html vtkMimxExtractCellWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractEdgeWidget.html vtkMimxExtractEdgeWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractFaceWidget.html vtkMimxExtractFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractMultipleFaceWidget.html vtkMimxExtractMultipleFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxModPointWidget.html vtkMimxModPointWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlaceLocalAxesWidget.html vtkMimxPlaceLocalAxesWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataWidget.html vtkMimxPolyDataWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidgetFEMesh.html vtkMimxSelectCellsWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidget.html vtkMimxSelectCellsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectPointsWidget.html vtkMimxSelectPointsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTraceContourWidget.html vtkMimxTraceContourWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridExtractWidget.html vtkMimxUnstructuredGridExtractWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridWidget.html vtkMimxUnstructuredGridWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxViewMergePointsWidget.html vtkMimxViewMergePointsWidget]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=13033 Modules:IA FEMesh-Documentation-3.6 2010-04-01T20:39:47Z <p>Vmagnotta: /* IA_FEMesh */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[IAFEmeshSlicer3Wizard.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[IAFEMESHWithSpine.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *'''Common'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]<br /> <br /> *'''Filter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFaceHedgeHog.html vtkFaceHedgeHog]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityExtended.html vtkMeshQualityExtended]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAddUnstructuredHexahedronGridCell.html vtkMimxAddUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyImageBasedMaterialProperties.html vtkMimxApplyImageBasedMaterialProperties]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAttachBoundingBoxMesh.html vtkMimxAttachBoundingBoxMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromBounds.html vtkMimxBoundingBoxFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromUnstructuredGrid.html vtkMimxBoundingBoxFromUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSurfaceMesh.html vtkMimxBoundingBoxSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxToStructuredGrids.html vtkMimxBoundingBoxToStructuredGrids]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxButterflyMeshFromBounds.html vtkMimxButterflyMeshFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxClipImageFromBox.html vtkMimxClipImageFromBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxComputeNormalsFromPolydataFilter.html vtkMimxComputeNormalsFromPolydataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxConstrainedSmoothPolyDataFilter.html vtkMimxConstrainedSmoothPolyDataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCylindricalMesh.html vtkMimxCylindricalMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxDeleteUnstructuredHexahedronGridCell.html vtkMimxDeleteUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToPlanarStructuredGrid.html vtkMimxEdgeToPlanarStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToStructuredGrid.html vtkMimxEdgeToStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEditUnstructuredHexahedronGrid.html vtkMimxEditUnstructuredHexahedronGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEquivalancePoints.html vtkMimxEquivalancePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractElementNumbersOfaFaceFilter.html vtkMimxExtractElementNumbersOfaFaceFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridEdge.html vtkMimxExtractStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridFace.html vtkMimxExtractStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractSurface.html vtkMimxExtractSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtrudePolyData.html vtkMimxExtrudePolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFilterWin32Header.html vtkMimxFilterWin32Header]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFourPointsToStructuredPlanarMesh.html vtkMimxFourPointsToStructuredPlanarMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGenerateHexahedronMesh.html vtkMimxGenerateHexahedronMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGeometryFilter.html vtkMimxGeometryFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMapOriginalCellAndPointIds.html vtkMimxMapOriginalCellAndPointIds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergePoints.html vtkMimxMergePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMirrorUnstructuredHexahedronGridCell.html vtkMimxMirrorUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMorphStructuredGrid.html vtkMimxMorphStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPatchSurfaceMesh.html vtkMimxPatchSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarEllipticalInterpolation.html vtkMimxPlanarEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTransfiniteInterpolation.html vtkMimxPlanarTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTrilinearInterpolation.html vtkMimxPlanarTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataSingleSourceShortestPath.html vtkMimxPolyDataSingleSourceShortestPath]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRebinMaterialProperty.html vtkMimxRebinMaterialProperty]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodes.html vtkMimxRecalculateInteriorNodes]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodesTPS.html vtkMimxRecalculateInteriorNodesTPS]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectSurface.html vtkMimxSelectSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridEdge.html vtkMimxSetStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridFace.html vtkMimxSetStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSmoothUnstructuredGridFilter.html vtkMimxSmoothUnstructuredGridFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidEllipticalInterpolation.html vtkMimxSolidEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTransfiniteInterpolation.html vtkMimxSolidTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTrilinearInterpolation.html vtkMimxSolidTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSplitUnstructuredHexahedronGridCell.html vtkMimxSplitUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxStructuredPlanarToStructuredSolidGrid.html vtkMimxStructuredPlanarToStructuredSolidGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideBoundingBox.html vtkMimxSubdivideBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideCurve.html vtkMimxSubdivideCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromBoundingBox.html vtkMimxUnstructuredGridFromBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromFourPoints.html vtkMimxUnstructuredGridFromFourPoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredToStructuredGrid.html vtkMimxUnstructuredToStructuredGrid]<br /> <br /> *'''IO'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1itkMimxAbaqusMeshFileWriter.html itkMimxAbaqusMeshFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ReadHistogramBinValuesFilter.html itkMimxReadHistogramBinValuesFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> '''Adapter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ItkMeshToFEMMesh.html ItkMeshToFEMMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkPolyData.html itkMeshTovtkPolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkUnstructuredGrid.html itkMeshTovtkUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPolyDataToitkMesh.html vtkPolyDataToitkMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkUnstructuredGridToitkMesh.html vtkUnstructuredGridToitkMesh]<br /> <br /> *'''Widgets'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxWidget.html vtkMimxBoundingBoxWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBWidgetPlusIPWidget.html vtkMimxBWidgetPlusIPWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateBuildingBlockFromPickWidget.html vtkMimxCreateBuildingBlockFromPickWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateElementSetWidgetFEMesh.html vtkMimxCreateElementSetWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractCellWidget.html vtkMimxExtractCellWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractEdgeWidget.html vtkMimxExtractEdgeWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractFaceWidget.html vtkMimxExtractFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractMultipleFaceWidget.html vtkMimxExtractMultipleFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxModPointWidget.html vtkMimxModPointWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlaceLocalAxesWidget.html vtkMimxPlaceLocalAxesWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataWidget.html vtkMimxPolyDataWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidgetFEMesh.html vtkMimxSelectCellsWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidget.html vtkMimxSelectCellsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectPointsWidget.html vtkMimxSelectPointsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTraceContourWidget.html vtkMimxTraceContourWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridExtractWidget.html vtkMimxUnstructuredGridExtractWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridWidget.html vtkMimxUnstructuredGridWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxViewMergePointsWidget.html vtkMimxViewMergePointsWidget]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=File:IAFEMESHWithSpine.png&diff=13032 File:IAFEMESHWithSpine.png 2010-04-01T20:38:59Z <p>Vmagnotta: </p> <hr /> <div></div> Vmagnotta https://www.slicer.org/w/index.php?title=File:IAFEmeshSlicer3Wizard.png&diff=13031 File:IAFEmeshSlicer3Wizard.png 2010-04-01T20:38:14Z <p>Vmagnotta: </p> <hr /> <div></div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12734 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:57:04Z <p>Vmagnotta: /* Source code &amp; documentation */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *'''Common'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]<br /> <br /> *'''Filter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFaceHedgeHog.html vtkFaceHedgeHog]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityExtended.html vtkMeshQualityExtended]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAddUnstructuredHexahedronGridCell.html vtkMimxAddUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyImageBasedMaterialProperties.html vtkMimxApplyImageBasedMaterialProperties]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAttachBoundingBoxMesh.html vtkMimxAttachBoundingBoxMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromBounds.html vtkMimxBoundingBoxFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromUnstructuredGrid.html vtkMimxBoundingBoxFromUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSurfaceMesh.html vtkMimxBoundingBoxSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxToStructuredGrids.html vtkMimxBoundingBoxToStructuredGrids]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxButterflyMeshFromBounds.html vtkMimxButterflyMeshFromBounds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxClipImageFromBox.html vtkMimxClipImageFromBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxComputeNormalsFromPolydataFilter.html vtkMimxComputeNormalsFromPolydataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxConstrainedSmoothPolyDataFilter.html vtkMimxConstrainedSmoothPolyDataFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCylindricalMesh.html vtkMimxCylindricalMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxDeleteUnstructuredHexahedronGridCell.html vtkMimxDeleteUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToPlanarStructuredGrid.html vtkMimxEdgeToPlanarStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToStructuredGrid.html vtkMimxEdgeToStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEditUnstructuredHexahedronGrid.html vtkMimxEditUnstructuredHexahedronGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEquivalancePoints.html vtkMimxEquivalancePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractElementNumbersOfaFaceFilter.html vtkMimxExtractElementNumbersOfaFaceFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridEdge.html vtkMimxExtractStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridFace.html vtkMimxExtractStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractSurface.html vtkMimxExtractSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtrudePolyData.html vtkMimxExtrudePolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFilterWin32Header.html vtkMimxFilterWin32Header]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFourPointsToStructuredPlanarMesh.html vtkMimxFourPointsToStructuredPlanarMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGenerateHexahedronMesh.html vtkMimxGenerateHexahedronMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGeometryFilter.html vtkMimxGeometryFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMapOriginalCellAndPointIds.html vtkMimxMapOriginalCellAndPointIds]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergePoints.html vtkMimxMergePoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMirrorUnstructuredHexahedronGridCell.html vtkMimxMirrorUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMorphStructuredGrid.html vtkMimxMorphStructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPatchSurfaceMesh.html vtkMimxPatchSurfaceMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarEllipticalInterpolation.html vtkMimxPlanarEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTransfiniteInterpolation.html vtkMimxPlanarTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTrilinearInterpolation.html vtkMimxPlanarTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataSingleSourceShortestPath.html vtkMimxPolyDataSingleSourceShortestPath]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRebinMaterialProperty.html vtkMimxRebinMaterialProperty]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodes.html vtkMimxRecalculateInteriorNodes]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodesTPS.html vtkMimxRecalculateInteriorNodesTPS]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectSurface.html vtkMimxSelectSurface]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridEdge.html vtkMimxSetStructuredGridEdge]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridFace.html vtkMimxSetStructuredGridFace]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSmoothUnstructuredGridFilter.html vtkMimxSmoothUnstructuredGridFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidEllipticalInterpolation.html vtkMimxSolidEllipticalInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTransfiniteInterpolation.html vtkMimxSolidTransfiniteInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTrilinearInterpolation.html vtkMimxSolidTrilinearInterpolation]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSplitUnstructuredHexahedronGridCell.html vtkMimxSplitUnstructuredHexahedronGridCell]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxStructuredPlanarToStructuredSolidGrid.html vtkMimxStructuredPlanarToStructuredSolidGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideBoundingBox.html vtkMimxSubdivideBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideCurve.html vtkMimxSubdivideCurve]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromBoundingBox.html vtkMimxUnstructuredGridFromBoundingBox]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromFourPoints.html vtkMimxUnstructuredGridFromFourPoints]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredToStructuredGrid.html vtkMimxUnstructuredToStructuredGrid]<br /> <br /> *'''IO'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1itkMimxAbaqusMeshFileWriter.html itkMimxAbaqusMeshFileWriter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ReadHistogramBinValuesFilter.html itkMimxReadHistogramBinValuesFilter]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> '''Adapter'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ItkMeshToFEMMesh.html ItkMeshToFEMMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkPolyData.html itkMeshTovtkPolyData]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkUnstructuredGrid.html itkMeshTovtkUnstructuredGrid]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPolyDataToitkMesh.html vtkPolyDataToitkMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkUnstructuredGridToitkMesh.html vtkUnstructuredGridToitkMesh]<br /> <br /> *'''Widgets'''<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxWidget.html vtkMimxBoundingBoxWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBWidgetPlusIPWidget.html vtkMimxBWidgetPlusIPWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateBuildingBlockFromPickWidget.html vtkMimxCreateBuildingBlockFromPickWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateElementSetWidgetFEMesh.html vtkMimxCreateElementSetWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractCellWidget.html vtkMimxExtractCellWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractEdgeWidget.html vtkMimxExtractEdgeWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractFaceWidget.html vtkMimxExtractFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractMultipleFaceWidget.html vtkMimxExtractMultipleFaceWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxModPointWidget.html vtkMimxModPointWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlaceLocalAxesWidget.html vtkMimxPlaceLocalAxesWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataWidget.html vtkMimxPolyDataWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidgetFEMesh.html vtkMimxSelectCellsWidgetFEMesh]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidget.html vtkMimxSelectCellsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectPointsWidget.html vtkMimxSelectPointsWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTraceContourWidget.html vtkMimxTraceContourWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridExtractWidget.html vtkMimxUnstructuredGridExtractWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridWidget.html vtkMimxUnstructuredGridWidget]<br /> **[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxViewMergePointsWidget.html vtkMimxViewMergePointsWidget]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12732 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:53:58Z <p>Vmagnotta: /* Source code &amp; documentation */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> '''Common'''<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]<br /> <br /> '''Filter'''<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFaceHedgeHog.html vtkFaceHedgeHog]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityExtended.html vtkMeshQualityExtended]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAddUnstructuredHexahedronGridCell.html vtkMimxAddUnstructuredHexahedronGridCell]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyImageBasedMaterialProperties.html vtkMimxApplyImageBasedMaterialProperties]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAttachBoundingBoxMesh.html vtkMimxAttachBoundingBoxMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromBounds.html vtkMimxBoundingBoxFromBounds]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromUnstructuredGrid.html vtkMimxBoundingBoxFromUnstructuredGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSurfaceMesh.html vtkMimxBoundingBoxSurfaceMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxToStructuredGrids.html vtkMimxBoundingBoxToStructuredGrids]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxButterflyMeshFromBounds.html vtkMimxButterflyMeshFromBounds]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxClipImageFromBox.html vtkMimxClipImageFromBox]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxComputeNormalsFromPolydataFilter.html vtkMimxComputeNormalsFromPolydataFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxConstrainedSmoothPolyDataFilter.html vtkMimxConstrainedSmoothPolyDataFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCylindricalMesh.html vtkMimxCylindricalMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxDeleteUnstructuredHexahedronGridCell.html vtkMimxDeleteUnstructuredHexahedronGridCell]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToPlanarStructuredGrid.html vtkMimxEdgeToPlanarStructuredGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToStructuredGrid.html vtkMimxEdgeToStructuredGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEditUnstructuredHexahedronGrid.html vtkMimxEditUnstructuredHexahedronGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEquivalancePoints.html vtkMimxEquivalancePoints]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractElementNumbersOfaFaceFilter.html vtkMimxExtractElementNumbersOfaFaceFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridEdge.html vtkMimxExtractStructuredGridEdge]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridFace.html vtkMimxExtractStructuredGridFace]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractSurface.html vtkMimxExtractSurface]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtrudePolyData.html vtkMimxExtrudePolyData]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFilterWin32Header.html vtkMimxFilterWin32Header]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFourPointsToStructuredPlanarMesh.html vtkMimxFourPointsToStructuredPlanarMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGenerateHexahedronMesh.html vtkMimxGenerateHexahedronMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGeometryFilter.html vtkMimxGeometryFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMapOriginalCellAndPointIds.html vtkMimxMapOriginalCellAndPointIds]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergePoints.html vtkMimxMergePoints]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMirrorUnstructuredHexahedronGridCell.html vtkMimxMirrorUnstructuredHexahedronGridCell]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMorphStructuredGrid.html vtkMimxMorphStructuredGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPatchSurfaceMesh.html vtkMimxPatchSurfaceMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarEllipticalInterpolation.html vtkMimxPlanarEllipticalInterpolation]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTransfiniteInterpolation.html vtkMimxPlanarTransfiniteInterpolation]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTrilinearInterpolation.html vtkMimxPlanarTrilinearInterpolation]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataSingleSourceShortestPath.html vtkMimxPolyDataSingleSourceShortestPath]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRebinMaterialProperty.html vtkMimxRebinMaterialProperty]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodes.html vtkMimxRecalculateInteriorNodes]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodesTPS.html vtkMimxRecalculateInteriorNodesTPS]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectSurface.html vtkMimxSelectSurface]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridEdge.html vtkMimxSetStructuredGridEdge]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridFace.html vtkMimxSetStructuredGridFace]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSmoothUnstructuredGridFilter.html vtkMimxSmoothUnstructuredGridFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidEllipticalInterpolation.html vtkMimxSolidEllipticalInterpolation]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTransfiniteInterpolation.html vtkMimxSolidTransfiniteInterpolation]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTrilinearInterpolation.html vtkMimxSolidTrilinearInterpolation]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSplitUnstructuredHexahedronGridCell.html vtkMimxSplitUnstructuredHexahedronGridCell]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxStructuredPlanarToStructuredSolidGrid.html vtkMimxStructuredPlanarToStructuredSolidGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideBoundingBox.html vtkMimxSubdivideBoundingBox]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideCurve.html vtkMimxSubdivideCurve]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromBoundingBox.html vtkMimxUnstructuredGridFromBoundingBox]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromFourPoints.html vtkMimxUnstructuredGridFromFourPoints]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredToStructuredGrid.html vtkMimxUnstructuredToStructuredGrid]<br /> <br /> ''IO''<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1itkMimxAbaqusMeshFileWriter.html itkMimxAbaqusMeshFileWriter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ReadHistogramBinValuesFilter.html itkMimxReadHistogramBinValuesFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> '''Adapter'''<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ItkMeshToFEMMesh.html ItkMeshToFEMMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkPolyData.html itkMeshTovtkPolyData]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkUnstructuredGrid.html itkMeshTovtkUnstructuredGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPolyDataToitkMesh.html vtkPolyDataToitkMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkUnstructuredGridToitkMesh.html vtkUnstructuredGridToitkMesh]<br /> <br /> '''Widgets'''<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxWidget.html vtkMimxBoundingBoxWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBWidgetPlusIPWidget.html vtkMimxBWidgetPlusIPWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateBuildingBlockFromPickWidget.html vtkMimxCreateBuildingBlockFromPickWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateElementSetWidgetFEMesh.html vtkMimxCreateElementSetWidgetFEMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractCellWidget.html vtkMimxExtractCellWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractEdgeWidget.html vtkMimxExtractEdgeWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractFaceWidget.html vtkMimxExtractFaceWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractMultipleFaceWidget.html vtkMimxExtractMultipleFaceWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxModPointWidget.html vtkMimxModPointWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlaceLocalAxesWidget.html vtkMimxPlaceLocalAxesWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataWidget.html vtkMimxPolyDataWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidgetFEMesh.html vtkMimxSelectCellsWidgetFEMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidget.html vtkMimxSelectCellsWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectPointsWidget.html vtkMimxSelectPointsWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTraceContourWidget.html vtkMimxTraceContourWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridExtractWidget.html vtkMimxUnstructuredGridExtractWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridWidget.html vtkMimxUnstructuredGridWidget]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxViewMergePointsWidget.html vtkMimxViewMergePointsWidget]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12731 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:42:52Z <p>Vmagnotta: /* Source code &amp; documentation */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> '''Common'''<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]<br /> <br /> '''Filter'''<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFaceHedgeHog.html vtkFaceHedgeHog]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityExtended.html vtkMeshQualityExtended]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAddUnstructuredHexahedronGridCell.html vtkMimxAddUnstructuredHexahedronGridCell]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyImageBasedMaterialProperties.html vtkMimxApplyImageBasedMaterialProperties]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAttachBoundingBoxMesh.html vtkMimxAttachBoundingBoxMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromBounds.html vtkMimxBoundingBoxFromBounds]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromUnstructuredGrid.html vtkMimxBoundingBoxFromUnstructuredGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSurfaceMesh.html vtkMimxBoundingBoxSurfaceMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxToStructuredGrids.html vtkMimxBoundingBoxToStructuredGrids]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxButterflyMeshFromBounds.html vtkMimxButterflyMeshFromBounds]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxClipImageFromBox.html vtkMimxClipImageFromBox]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxComputeNormalsFromPolydataFilter.html vtkMimxComputeNormalsFromPolydataFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxConstrainedSmoothPolyDataFilter.html vtkMimxConstrainedSmoothPolyDataFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCylindricalMesh.html vtkMimxCylindricalMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxDeleteUnstructuredHexahedronGridCell.html vtkMimxDeleteUnstructuredHexahedronGridCell]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToPlanarStructuredGrid.html vtkMimxEdgeToPlanarStructuredGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToStructuredGrid.html vtkMimxEdgeToStructuredGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEditUnstructuredHexahedronGrid.html vtkMimxEditUnstructuredHexahedronGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEquivalancePoints.html vtkMimxEquivalancePoints]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractElementNumbersOfaFaceFilter.html vtkMimxExtractElementNumbersOfaFaceFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridEdge.html vtkMimxExtractStructuredGridEdge]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridFace.html vtkMimxExtractStructuredGridFace]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractSurface.html vtkMimxExtractSurface]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtrudePolyData.html vtkMimxExtrudePolyData]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFilterWin32Header.html vtkMimxFilterWin32Header]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFourPointsToStructuredPlanarMesh.html vtkMimxFourPointsToStructuredPlanarMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGenerateHexahedronMesh.html vtkMimxGenerateHexahedronMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGeometryFilter.html vtkMimxGeometryFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMapOriginalCellAndPointIds.html vtkMimxMapOriginalCellAndPointIds]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergePoints.html vtkMimxMergePoints]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMirrorUnstructuredHexahedronGridCell.html vtkMimxMirrorUnstructuredHexahedronGridCell]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMorphStructuredGrid.html vtkMimxMorphStructuredGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPatchSurfaceMesh.html vtkMimxPatchSurfaceMesh]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarEllipticalInterpolation.html vtkMimxPlanarEllipticalInterpolation]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTransfiniteInterpolation.html vtkMimxPlanarTransfiniteInterpolation]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTrilinearInterpolation.html vtkMimxPlanarTrilinearInterpolation]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataSingleSourceShortestPath.html vtkMimxPolyDataSingleSourceShortestPath]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRebinMaterialProperty.html vtkMimxRebinMaterialProperty]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodes.html vtkMimxRecalculateInteriorNodes]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodesTPS.html vtkMimxRecalculateInteriorNodesTPS]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectSurface.html vtkMimxSelectSurface]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridEdge.html vtkMimxSetStructuredGridEdge]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridFace.html vtkMimxSetStructuredGridFace]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSmoothUnstructuredGridFilter.html vtkMimxSmoothUnstructuredGridFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidEllipticalInterpolation.html vtkMimxSolidEllipticalInterpolation]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTransfiniteInterpolation.html vtkMimxSolidTransfiniteInterpolation]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTrilinearInterpolation.html vtkMimxSolidTrilinearInterpolation]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSplitUnstructuredHexahedronGridCell.html vtkMimxSplitUnstructuredHexahedronGridCell]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxStructuredPlanarToStructuredSolidGrid.html vtkMimxStructuredPlanarToStructuredSolidGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideBoundingBox.html vtkMimxSubdivideBoundingBox]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideCurve.html vtkMimxSubdivideCurve]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromBoundingBox.html vtkMimxUnstructuredGridFromBoundingBox]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromFourPoints.html vtkMimxUnstructuredGridFromFourPoints]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredToStructuredGrid.html vtkMimxUnstructuredToStructuredGrid]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12730 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:34:41Z <p>Vmagnotta: /* Source code &amp; documentation */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12729 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:30:13Z <p>Vmagnotta: /* Source code &amp; documentation */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classmimxApplyNodeElementNumbers.html mimxApplyNodeElementNumbers]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html mimxCheckTypeOfFile]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html mimxCommonDefine]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html mimxCreateIntervertebralDiscElementSets]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html mimxFileNames]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html mimxIncludeFileNames]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html mimxLinkedList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html mimxMatrixTemplate]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html mimxMergeNodesPointAndCellData]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html mimxMeshSeed]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html mimxRegisterBSplineFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html mimxRegisterVersorRigidFilter]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html mimxTransformIO]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkAbstractIterator]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkAbstractList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkContainer]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkFESurfaceList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkFiniteElementBuildingBlockList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkFiniteElementMeshList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkLinkedList]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkLinkedListIterator]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkLinkedListWrapper]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkLinkedListWrapperTree]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkLocalAxesActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkLocalLinkedListWrapper]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMeshQualityClass]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxActorBase]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxApplyNodeElementNumbers]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxBoundaryConditionActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxBoundingBoxSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxColorCodeMeshSeedActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxCommonWin32Header]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxCreateIntervertebralDiscElementSets]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxCurve]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxEntryValueChangedCallback]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxErrorCallback]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxImageActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxInteractorStyleUser]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxMergeNodesPointAndCellData]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxMeshActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxMeshSeed]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxPlanarStructuredGridSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxSolidStructuredGridSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxSTLSource]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxSurfacePolyDataActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxTestErrorCallback]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxUGrid]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxUnstructuredGridActor]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMRMLFESurfaceNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMRMLFiniteElementBuildingBlockDisplayNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMRMLFiniteElementBuildingBlockNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMRMLFiniteElementMeshDisplayNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMRMLFiniteElementMeshNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMRMLNullDisplayNode]<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkPVAxesActor]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12728 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:20:01Z <p>Vmagnotta: /* IA_FEMesh */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=File:IAMeshResult1.png&diff=12727 File:IAMeshResult1.png 2010-03-26T14:19:23Z <p>Vmagnotta: </p> <hr /> <div></div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12726 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:17:51Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]<br /> * Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12725 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:14:21Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and Psychiatry, [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]<br /> * Steve Pieper: Isomics <br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12724 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:09:46Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of Biomedical Engineering and Orthopaedic Surgery, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Vincent Magnotta: The University of Iowa - Departments of Radiology, Biomedical Engineering and Psychiatry, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Kiran Shivanna: The University of Iowa - Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Austin Ramme: The University of Iowa - Department of Biomedical Engineering, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Steve Pieper: Isomics <br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> <br /> {|<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]<br /> |[[Image:LogoIsomics.gif|thumb|100px|Isomics]]<br /> |[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12723 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:07:54Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> {|<br /> |<br /> * Nicole Grosland: The University of Iowa - Departments of Biomedical Engineering and Orthopaedic Surgery, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Vincent Magnotta: The University of Iowa - Departments of Radiology, Biomedical Engineering and Psychiatry, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Kiran Shivanna: The University of Iowa - Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Austin Ramme: The University of Iowa - Department of Biomedical Engineering, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Steve Pieper: Isomics <br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]] [[Image:LogoIsomics.gif|thumb|100px|Isomics]] [[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12722 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:07:16Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> {|<br /> |<br /> * Nicole Grosland: The University of Iowa - Departments of Biomedical Engineering and Orthopaedic Surgery, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Vincent Magnotta: The University of Iowa - Departments of Radiology, Biomedical Engineering and Psychiatry, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Kiran Shivanna: The University of Iowa - Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Steve Pieper: Isomics <br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> |[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]] [[Image:LogoIsomics.gif|thumb|100px|Isomics]] [[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12721 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:06:38Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> {|<br /> |<br /> * Nicole Grosland: The University of Iowa - Departments of Biomedical Engineering and Orthopaedic Surgery, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Vincent Magnotta: The University of Iowa - Departments of Radiology, Biomedical Engineering and Psychiatry, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Kiran Shivanna: The University of Iowa - Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Steve Pieper: Isomics <br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> |[[Image:LogoMimx.gif|thumb|100px|MIMX]] [[Image:LogoIsomics.gif|thumb|100px|MIMX]] [[Image:logoKvis.jpg|thumb|100px|MIMX]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12720 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:06:14Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> {|<br /> |<br /> * Nicole Grosland: The University of Iowa - Departments of Biomedical Engineering and Orthopaedic Surgery, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Vincent Magnotta: The University of Iowa - Departments of Radiology, Biomedical Engineering and Psychiatry, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Kiran Shivanna: The University of Iowa - Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Steve Pieper: Isomics <br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> |[[Image:LogoMimx.gif|thumb|100px|MIMX]] [[Image:LogoIsomics.gif|thumb|100px|MIMX]] [[Image:LogoKvis.gif|thumb|100px|MIMX]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=File:LogoKvis.jpg&diff=12719 File:LogoKvis.jpg 2010-03-26T14:05:49Z <p>Vmagnotta: </p> <hr /> <div></div> Vmagnotta https://www.slicer.org/w/index.php?title=File:LogoIsomics.gif&diff=12718 File:LogoIsomics.gif 2010-03-26T14:05:33Z <p>Vmagnotta: </p> <hr /> <div></div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12717 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:05:00Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> {|<br /> |<br /> * Nicole Grosland: The University of Iowa - Departments of Biomedical Engineering and Orthopaedic Surgery, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Vincent Magnotta: The University of Iowa - Departments of Radiology, Biomedical Engineering and Psychiatry, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Kiran Shivanna: The University of Iowa - Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Steve Pieper: Isomics <br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> |[[Image:LogoMimx.gif|thumb|100px|MIMX]] [[Image:LogoMimx.gif|thumb|100px|MIMX]] [[Image:LogoMimx.gif|thumb|100px|MIMX]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12716 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:04:48Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> {|<br /> |<br /> * Nicole Grosland: The University of Iowa - Departments of Biomedical Engineering and Orthopaedic Surgery, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX) [[Image:LogoMimx.gif|thumb|100px|MIMX]]<br /> * Vincent Magnotta: The University of Iowa - Departments of Radiology, Biomedical Engineering and Psychiatry, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Kiran Shivanna: The University of Iowa - Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Steve Pieper: Isomics <br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> |[[Image:LogoMimx.gif|thumb|100px|MIMX]] [[Image:LogoMimx.gif|thumb|100px|MIMX]] [[Image:LogoMimx.gif|thumb|100px|MIMX]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12715 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:03:41Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> {|<br /> * Nicole Grosland: The University of Iowa - Departments of Biomedical Engineering and Orthopaedic Surgery, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX) [[Image:LogoMimx.gif|thumb|100px|MIMX]]<br /> * Vincent Magnotta: The University of Iowa - Departments of Radiology, Biomedical Engineering and Psychiatry, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Kiran Shivanna: The University of Iowa - Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Steve Pieper: Isomics <br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> |[[Image:LogoMimx.gif|thumb|100px|MIMX]] [[Image:LogoMimx.gif|thumb|100px|MIMX]] [[Image:LogoMimx.gif|thumb|100px|MIMX]]<br /> |}<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12714 Modules:IA FEMesh-Documentation-3.6 2010-03-26T14:02:15Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Departments of Biomedical Engineering and Orthopaedic Surgery, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX) [[Image:LogoMimx.gif|thumb|100px|MIMX]]<br /> * Vincent Magnotta: The University of Iowa - Departments of Radiology, Biomedical Engineering and Psychiatry, Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Kiran Shivanna: The University of Iowa - Center for Computer Aided Design (CCAD), Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)<br /> * Steve Pieper: Isomics - [[Image:LogoMimx.gif|thumb|100px|MIMX]]<br /> * Curt Lisle: KnowledgeViz - [[Image:LogoMimx.gif|thumb|100px|MIMX]]<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12713 Modules:IA FEMesh-Documentation-3.6 2010-03-26T13:57:56Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - [[Image:LogoMimx.gif|thumb|100px|MIMX]]<br /> * Vincent Magnotta: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Kiran Shivanna: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Steve Pieper: Isomics - Affiliation &amp; logo, if desired<br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12712 Modules:IA FEMesh-Documentation-3.6 2010-03-26T13:57:21Z <p>Vmagnotta: /* Authors, Collaborators &amp; Contact */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - [[Image:MimxLogo|thumb|100px|MIMX]]<br /> * Vincent Magnotta: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Kiran Shivanna: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Steve Pieper: Isomics - Affiliation &amp; logo, if desired<br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=File:LogoMimx.gif&diff=12711 File:LogoMimx.gif 2010-03-26T13:55:51Z <p>Vmagnotta: </p> <hr /> <div></div> Vmagnotta https://www.slicer.org/w/index.php?title=File:Logo_mimx.gif&diff=12710 File:Logo mimx.gif 2010-03-26T13:55:28Z <p>Vmagnotta: </p> <hr /> <div></div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12709 Modules:IA FEMesh-Documentation-3.6 2010-03-26T13:53:59Z <p>Vmagnotta: /* Acknowledgment */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Vincent Magnotta: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Kiran Shivanna: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Steve Pieper: Isomics - Affiliation &amp; logo, if desired<br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12708 Modules:IA FEMesh-Documentation-3.6 2010-03-26T13:48:06Z <p>Vmagnotta: /* Source code &amp; documentation */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Vincent Magnotta: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Kiran Shivanna: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Steve Pieper: Isomics - Affiliation &amp; logo, if desired<br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12707 Modules:IA FEMesh-Documentation-3.6 2010-03-26T13:47:33Z <p>Vmagnotta: /* Source code &amp; documentation */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Vincent Magnotta: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Kiran Shivanna: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Steve Pieper: Isomics - Affiliation &amp; logo, if desired<br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> Source code:<br /> [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh]<br /> It consists of several subdirectories:<br /> *Adapter - Converts between ITK and VTK data structures<br /> *BuildingBlock - Classes to implement the KWWidgets user interface<br /> *Common - Custom data structures used for the meshing algorithms<br /> *Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.<br /> *IA_FEMesh - Loadable module for meshing<br /> *IO - Loading and saving of data<br /> *Mesh - Meshing routines implemented using ITK<br /> *Testing - Testing infrastructure<br /> *Widgets - Custom 3D VTK widgets to support user interaction during mesh generation<br /> <br /> Source code:<br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12706 Modules:IA FEMesh-Documentation-3.6 2010-03-26T13:39:15Z <p>Vmagnotta: /* Quick Tour of Features and Use */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Vincent Magnotta: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Kiran Shivanna: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Steve Pieper: Isomics - Affiliation &amp; logo, if desired<br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> Links to the module's source code:<br /> <br /> Source code:<br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12705 Modules:IA FEMesh-Documentation-3.6 2010-03-26T13:38:59Z <p>Vmagnotta: /* Quick Tour of Features and Use */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Vincent Magnotta: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Kiran Shivanna: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Steve Pieper: Isomics - Affiliation &amp; logo, if desired<br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:MeshingTabs.png.png|thumb|280px|IA-FEMesh Tabbed Wizard Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> Links to the module's source code:<br /> <br /> Source code:<br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=File:MeshingTabs.png&diff=12704 File:MeshingTabs.png 2010-03-26T13:38:10Z <p>Vmagnotta: </p> <hr /> <div></div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12702 Modules:IA FEMesh-Documentation-3.6 2010-03-26T13:35:36Z <p>Vmagnotta: /* Quick Tour of Features and Use */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Vincent Magnotta: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Kiran Shivanna: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Steve Pieper: Isomics - Affiliation &amp; logo, if desired<br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.<br /> <br /> {|<br /> |<br /> * '''Image:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> * '''Surface:'''<br /> ** '''Load'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Block(s):'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Build/Edit'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Mesh:'''<br /> ** '''Assign/Edit Mesh Seeds'''<br /> ** '''Create'''<br /> ** '''Load'''<br /> ** '''Renumber Nodes/Elements'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Delete'''<br /> ** '''Save'''<br /> * '''Quality:'''<br /> ** '''Evaluate/Display Mesh Quality'''<br /> ** '''Mesh Improvement'''<br /> ** '''Export Abaqus File'''<br /> ** '''Save'''<br /> * '''Materials:'''<br /> ** '''User-Defined'''<br /> ** '''Image Based'''<br /> ** '''Display Material Properties'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> * '''Load/BC:'''<br /> ** '''Step - Load/BC Assignments'''<br /> ** '''Export ABAQUS File'''<br /> ** '''Save'''<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> Links to the module's source code:<br /> <br /> Source code:<br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12699 Modules:IA FEMesh-Documentation-3.6 2010-03-26T13:22:35Z <p>Vmagnotta: /* Tests */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Vincent Magnotta: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Kiran Shivanna: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Steve Pieper: Isomics - Affiliation &amp; logo, if desired<br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> A list panels in the interface, their features, what they mean, and how to use them. For instance:<br /> <br /> {|<br /> |<br /> * '''Input panel:'''<br /> ** '''First input'''<br /> ** '''Second input'''<br /> * '''Parameters panel:'''<br /> ** '''First parameter'''<br /> ** '''Second parameter'''<br /> * '''Output panel:'''<br /> ** '''First output'''<br /> ** '''Second output'''<br /> * '''Viewing panel:'''<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]<br /> * MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]<br /> * MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]<br /> * MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]<br /> * MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]<br /> * MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]<br /> * MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]<br /> * MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]<br /> * MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]<br /> * MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]<br /> * MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]<br /> * MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]<br /> * MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> Links to the module's source code:<br /> <br /> Source code:<br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12697 Modules:IA FEMesh-Documentation-3.6 2010-03-26T13:15:28Z <p>Vmagnotta: /* Tests */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Vincent Magnotta: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Kiran Shivanna: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Steve Pieper: Isomics - Affiliation &amp; logo, if desired<br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> A list panels in the interface, their features, what they mean, and how to use them. For instance:<br /> <br /> {|<br /> |<br /> * '''Input panel:'''<br /> ** '''First input'''<br /> ** '''Second input'''<br /> * '''Parameters panel:'''<br /> ** '''First parameter'''<br /> ** '''Second parameter'''<br /> * '''Output panel:'''<br /> ** '''First output'''<br /> ** '''Second output'''<br /> * '''Viewing panel:'''<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]<br /> <br /> * MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> Links to the module's source code:<br /> <br /> Source code:<br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta https://www.slicer.org/w/index.php?title=Modules:IA_FEMesh-Documentation-3.6&diff=12665 Modules:IA FEMesh-Documentation-3.6 2010-03-25T14:09:12Z <p>Vmagnotta: /* References */</p> <hr /> <div>[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br /> <br /> [[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br /> <br /> __NOTOC__<br /> ===IA_FEMesh===<br /> IA-FEMesh<br /> <br /> {|<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Output]]<br /> |[[Image:screenshotBlank.png|thumb|280px|Caption]]<br /> |}<br /> <br /> == General Information ==<br /> ===Module Type &amp; Category===<br /> <br /> Type: Interactive<br /> <br /> Category: Wizard<br /> <br /> ===Authors, Collaborators &amp; Contact===<br /> * Nicole Grosland: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Vincent Magnotta: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Kiran Shivanna: The University of Iowa - Affiliation &amp; logo, if desired<br /> * Steve Pieper: Isomics - Affiliation &amp; logo, if desired<br /> * Curt Lisle: KnowledgeViz<br /> * Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)<br /> <br /> ===Module Description===<br /> This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.<br /> <br /> == Usage ==<br /> <br /> ===Use Cases, Examples===<br /> <br /> The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:<br /> <br /> * '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed. <br /> * '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.<br /> * '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation. <br /> * '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired. <br /> * '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file. <br /> * '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.<br /> <br /> ===Tutorials===<br /> <br /> Links to tutorials explaining how to use this module:<br /> <br /> * [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]<br /> ** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]<br /> * [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]<br /> <br /> ===Quick Tour of Features and Use===<br /> <br /> A list panels in the interface, their features, what they mean, and how to use them. For instance:<br /> <br /> {|<br /> |<br /> * '''Input panel:'''<br /> ** '''First input'''<br /> ** '''Second input'''<br /> * '''Parameters panel:'''<br /> ** '''First parameter'''<br /> ** '''Second parameter'''<br /> * '''Output panel:'''<br /> ** '''First output'''<br /> ** '''Second output'''<br /> * '''Viewing panel:'''<br /> |[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]<br /> |}<br /> <br /> == Development ==<br /> <br /> ===Notes from the Developer(s)===<br /> <br /> Algorithms used, library classes depended upon, use cases, etc.<br /> <br /> ===Dependencies===<br /> <br /> * [http://www.itk.org ITK]<br /> * [http://www.vtk.org VTK]<br /> * [http://www.kwwidgets.org KWWidgets]<br /> <br /> ===Tests===<br /> <br /> On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br /> <br /> * MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]<br /> * MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]<br /> <br /> ===Known bugs===<br /> <br /> Links to known bugs in the Slicer3 bug tracker<br /> <br /> * [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description] <br /> <br /> <br /> ===Usability issues===<br /> <br /> Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br /> <br /> ===Source code &amp; documentation===<br /> <br /> Links to the module's source code:<br /> <br /> Source code:<br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ] <br /> *[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]<br /> <br /> Doxygen documentation:<br /> *[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]<br /> <br /> == More Information == <br /> <br /> ===Acknowledgment===<br /> This work is supported in part by NIH/NIBIB awards R01EB005973 and R21<br /> <br /> ===References===<br /> #Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br /> #Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br /> #Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br /> #Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br /> #Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br /> #Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br /> #DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br /> #Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br /> #Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br /> #Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br /> #Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br /> #Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br /> #Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.</div> Vmagnotta