https://www.slicer.org/w/api.php?action=feedcontributions&feedformat=atom&user=Fdrakopo Slicer Wiki - User contributions [en] 2026-05-07T02:01:00Z User contributions MediaWiki 1.33.0 https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/MeshCompression&diff=38468 Documentation/Nightly/Modules/MeshCompression 2014-06-27T02:37:42Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion |CBC 3D I2MConversion]]&lt;br&gt;<br /> Acknowledgments:<br /> *This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.<br /> <br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The Mesh Compression (MC) module deforms the input tetrahedral mesh towards the boundaries of the input labeled image. Two point sets are extracted for the mesh deformation. The first (source point set) consists of the surface vertices in the input mesh. The second (target point set) consists of the surface edge points in the input labeled image. After the extraction of the two point sets, the input mesh is deformed by registering the source to the target point set using a Physics-Based Non-Rigid Registration method. The current version of the module supports a single-tissue labeled image and mesh.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[File:brain_before.jpg|thumb|300px|Brain BCC mesh before MC]]<br /> |[[File:brain_after.jpg|thumb|300px|Brain BCC mesh after MC]]<br /> |[[File:brain_after_section.jpg|thumb|300px|Brain BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:nidus_before.jpg|thumb|300px|Nidus BCC mesh before MC]]<br /> |[[File:nidus_after.jpg|thumb|300px|Nidus BCC mesh after MC]]&lt;br&gt;<br /> |[[File:nidus_after_section.jpg|thumb|300px|Nidus BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:ventricles_before.jpg|thumb|300px|Ventricles BCC mesh before MC]]<br /> |[[File:ventricles_after.jpg|thumb|300px|Ventricles BCC mesh after MC]]<br /> |[[File:ventricles_after_section.jpg|thumb|300px|Ventricles BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:target_points.jpg|thumb|960px|How the non-connectivity parameter influences the number of the extracted target points]]<br /> |}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Mesh Compression Parameters:'''<br /> ** '''Flexibility:''' Controls the trade-off between the regularization energy defined by the stress energy of a linear bio-mechanical elastic model, and the similarity energy. Value should be between [0.1,1] (default: 1).<br /> ** '''Number of Iterations:''' Controls the number of iterations for the compressor. The larger the value the closer the boundaries of the input mesh to the boundaries of the input image. A large number of iterations might cause distorted poor-quality elements. Value should be between [1,10] (default: 3).<br /> ** '''Non Connectivity:''' Controls the density of the extracted target points via a prohibited connectivity between adjacent blocks of voxels. The larger the value the denser the target point set. 0 is vertex non-connectivity (26 neighbors), 1 is edge non-connectivity (18 neighbors), 2 is face non-connectivity (6 neighbors) and 3 is no non-connectivity. Value should be 0 or 1 or 2 or 3. (default: 0).<br /> * '''Input/Output:'''<br /> ** '''Input Labeled Image:''' The input labeled image.<br /> ** '''Input Mesh File:''' The input tetrahedral mesh in vtk file format.<br /> ** '''Output Mesh File:''' The output deformed mesh in vtk file format (optional) (default: deformedMesh.vtk).<br /> ** '''Output Source Points File:''' The extracted source points in vtk file format (optional). The source points are the surface vertices of the input mesh.<br /> ** '''Output Target Points File:''' The extracted target points in vtk file format (optional). The target points are the surface edge points of the input labeled image.<br /> ** '''Output Surface Triangles File:''' The extracted surface triangles of the input mesh in vtk file format (optional).<br /> |[[Image:MCPanel.jpg|thumb|380px|User Interface]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/BodyCentricCubicMesh]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/BodyCentricCubicMesh&diff=38467 Documentation/Nightly/Modules/BodyCentricCubicMesh 2014-06-27T02:37:11Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion |CBC 3D I2MConversion]]&lt;br&gt;<br /> Acknowledgments:<br /> *This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.<br /> <br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu<br /> &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module generates a Body Centric Cubic (BCC) mesh from a labeled image. Initially the generated mesh is homogeneous, that means does not distinguish different tissues. Later the module specifies which tissue each tetrahedron belongs to. Each tissue is capable of automatically adjusting its resolution based on its geometric complexity and the predefined subdivision criterion. The current version of the module supports a single-tissue input labeled image.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[File:brain.jpg|thumb|280px|Brain BCC mesh]]<br /> |[[File:nidus.jpg|thumb|280px|Nidus BCC mesh]]<br /> |[[File:ventricles.jpg|thumb|280px|Ventricles BCC mesh]]<br /> |}<br /> {|<br /> |[[File:brain_section.jpg|thumb|280px|Brain BCC mesh cross-section]]<br /> |[[File:nidus_section.jpg|thumb|280px|Nidus BCC mesh cross-section]]<br /> |[[File:ventricles_section.jpg|thumb|280px|Ventricles BCC mesh cross-section]]<br /> |}<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Mesh Generation Parameters:'''<br /> ** '''Size:''' Controls the size of the mesh. The smaller the value the larger the mesh. Value should be between [1,20] (default: 8).<br /> ** '''Fidelity:''' Controls the subdivision of the elements that belong to more than one image labels. The larger the value the better the conformity of the mesh on the image label boundaries. Value should be between [0.1,1] (default: 0.8).<br /> ** '''Resample Resolution:''' Controls the image resampling. Suggested value is 0 (no-resampling) for large tissues and 1 or 2 for smaller tissues. Value should be 0 or 1 or 2 (default: 0).<br /> * '''Input/Output:'''<br /> ** '''Input Labeled Image:''' The input labeled image.<br /> ** '''Output Mesh File:''' The output tetrahedral mesh in vtk file format. (default: outputMesh.vtk)<br /> |[[Image:BCCPanel.jpg|thumb|320px|User Interface]]<br /> |}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/MeshCompression]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CBC_3D_I2MConversion&diff=38466 Documentation/Nightly/Extensions/CBC 3D I2MConversion 2014-06-27T02:36:42Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion | CBC 3D I2MConversion]]&lt;br&gt;<br /> Acknowledgments:<br /> This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> '''CBC 3D I2MConversion''' stands for CRTC's BCC &amp; Compression Image-To-Mesh Conversion. '''CBC 3D I2MConversion''' is a software for generating high quality tetrahedral meshes from brain labeled images.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> *[[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Use Cases}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br /> N/A<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/extension-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CBC_3D_I2MConversion&diff=38465 Documentation/Nightly/Extensions/CBC 3D I2MConversion 2014-06-27T02:35:46Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion | CBC 3D I2MConversion]]&lt;br&gt;<br /> Acknowledgments:<br /> This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> '''CBC3DI2MConversion''' stands for CRTC's BCC &amp; Compression Image-To-Mesh Conversion. '''CBC3DI2MConversion''' is a software for generating high quality tetrahedral meshes from brain labeled images.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> *[[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Use Cases}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br /> N/A<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/extension-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions&diff=38464 Documentation/Nightly/Extensions 2014-06-27T02:34:51Z <p>Fdrakopo: /* Cat 2 */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;noinclude&gt;<br /> __TOC__<br /> &lt;/noinclude&gt;= Extensions by Category =<br /> <br /> ==Cat 1==<br /> <br /> ==Cat 2==<br /> *[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )<br /> * [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)<br /> * [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)<br /> * [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)<br /> * [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroImport|DICOM-SRO import]] --&gt;<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroExport|DICOM-SRO export]] --&gt;<br /> ** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy (integrated into Slicer trunk)]]<br /> ** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)<br /> ** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)<br /> ** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)<br /> ** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)<br /> * [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)<br /> * [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)<br /> * [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)<br /> * [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)<br /> * [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)<br /> * [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)<br /> ** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]<br /> * [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]<br /> * [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)<br /> * [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)<br /> * [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)<br /> * [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)<br /> **[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)<br /> * [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]<br /> ** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]<br /> ** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]<br /> * [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)<br /> * [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)<br /> * [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)<br /> * [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]<br /> * [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]] (Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion | CBC 3D I2MConversion]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)<br /> ** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> ** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz and Nikos Chrisochoides)<br /> <br /> ==Cat 3==<br /> * [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation-&gt;TrainModel]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation-&gt;PredictLesions]] (Mark Scully)<br /> * [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)<br /> * [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)<br /> &lt;noinclude&gt;<br /> {{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}<br /> &lt;/noinclude&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions&diff=38462 Documentation/Nightly/Extensions 2014-06-27T02:31:38Z <p>Fdrakopo: /* Cat 2 */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;noinclude&gt;<br /> __TOC__<br /> &lt;/noinclude&gt;= Extensions by Category =<br /> <br /> ==Cat 1==<br /> <br /> ==Cat 2==<br /> *[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )<br /> * [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)<br /> * [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)<br /> * [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)<br /> * [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroImport|DICOM-SRO import]] --&gt;<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroExport|DICOM-SRO export]] --&gt;<br /> ** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy (integrated into Slicer trunk)]]<br /> ** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)<br /> ** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)<br /> ** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)<br /> ** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)<br /> * [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)<br /> * [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)<br /> * [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)<br /> * [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)<br /> * [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)<br /> * [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)<br /> ** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]<br /> * [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]<br /> * [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)<br /> * [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)<br /> * [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)<br /> * [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)<br /> **[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)<br /> * [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]<br /> ** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]<br /> ** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]<br /> * [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)<br /> * [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)<br /> * [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)<br /> * [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]<br /> * [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]] (Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/CBC3DI2MConversion | CBC 3D I2MConversion]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)<br /> ** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> ** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz and Nikos Chrisochoides)<br /> <br /> ==Cat 3==<br /> * [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation-&gt;TrainModel]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation-&gt;PredictLesions]] (Mark Scully)<br /> * [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)<br /> * [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)<br /> &lt;noinclude&gt;<br /> {{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}<br /> &lt;/noinclude&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/MeshCompression&diff=38461 Documentation/Nightly/Modules/MeshCompression 2014-06-27T02:26:48Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/CBC3DI2MConversion |CBC3DI2MConversion]]&lt;br&gt;<br /> Acknowledgments:<br /> *This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.<br /> <br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The Mesh Compression (MC) module deforms the input tetrahedral mesh towards the boundaries of the input labeled image. Two point sets are extracted for the mesh deformation. The first (source point set) consists of the surface vertices in the input mesh. The second (target point set) consists of the surface edge points in the input labeled image. After the extraction of the two point sets, the input mesh is deformed by registering the source to the target point set using a Physics-Based Non-Rigid Registration method. The current version of the module supports a single-tissue labeled image and mesh.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[File:brain_before.jpg|thumb|300px|Brain BCC mesh before MC]]<br /> |[[File:brain_after.jpg|thumb|300px|Brain BCC mesh after MC]]<br /> |[[File:brain_after_section.jpg|thumb|300px|Brain BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:nidus_before.jpg|thumb|300px|Nidus BCC mesh before MC]]<br /> |[[File:nidus_after.jpg|thumb|300px|Nidus BCC mesh after MC]]&lt;br&gt;<br /> |[[File:nidus_after_section.jpg|thumb|300px|Nidus BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:ventricles_before.jpg|thumb|300px|Ventricles BCC mesh before MC]]<br /> |[[File:ventricles_after.jpg|thumb|300px|Ventricles BCC mesh after MC]]<br /> |[[File:ventricles_after_section.jpg|thumb|300px|Ventricles BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:target_points.jpg|thumb|960px|How the non-connectivity parameter influences the number of the extracted target points]]<br /> |}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Mesh Compression Parameters:'''<br /> ** '''Flexibility:''' Controls the trade-off between the regularization energy defined by the stress energy of a linear bio-mechanical elastic model, and the similarity energy. Value should be between [0.1,1] (default: 1).<br /> ** '''Number of Iterations:''' Controls the number of iterations for the compressor. The larger the value the closer the boundaries of the input mesh to the boundaries of the input image. A large number of iterations might cause distorted poor-quality elements. Value should be between [1,10] (default: 3).<br /> ** '''Non Connectivity:''' Controls the density of the extracted target points via a prohibited connectivity between adjacent blocks of voxels. The larger the value the denser the target point set. 0 is vertex non-connectivity (26 neighbors), 1 is edge non-connectivity (18 neighbors), 2 is face non-connectivity (6 neighbors) and 3 is no non-connectivity. Value should be 0 or 1 or 2 or 3. (default: 0).<br /> * '''Input/Output:'''<br /> ** '''Input Labeled Image:''' The input labeled image.<br /> ** '''Input Mesh File:''' The input tetrahedral mesh in vtk file format.<br /> ** '''Output Mesh File:''' The output deformed mesh in vtk file format (optional) (default: deformedMesh.vtk).<br /> ** '''Output Source Points File:''' The extracted source points in vtk file format (optional). The source points are the surface vertices of the input mesh.<br /> ** '''Output Target Points File:''' The extracted target points in vtk file format (optional). The target points are the surface edge points of the input labeled image.<br /> ** '''Output Surface Triangles File:''' The extracted surface triangles of the input mesh in vtk file format (optional).<br /> |[[Image:MCPanel.jpg|thumb|380px|User Interface]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/BodyCentricCubicMesh]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/BodyCentricCubicMesh&diff=38460 Documentation/Nightly/Modules/BodyCentricCubicMesh 2014-06-27T02:26:08Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/CBC3DI2MConversion |CBC3DI2MConversion]]&lt;br&gt;<br /> Acknowledgments:<br /> *This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.<br /> <br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu<br /> &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module generates a Body Centric Cubic (BCC) mesh from a labeled image. Initially the generated mesh is homogeneous, that means does not distinguish different tissues. Later the module specifies which tissue each tetrahedron belongs to. Each tissue is capable of automatically adjusting its resolution based on its geometric complexity and the predefined subdivision criterion. The current version of the module supports a single-tissue input labeled image.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[File:brain.jpg|thumb|280px|Brain BCC mesh]]<br /> |[[File:nidus.jpg|thumb|280px|Nidus BCC mesh]]<br /> |[[File:ventricles.jpg|thumb|280px|Ventricles BCC mesh]]<br /> |}<br /> {|<br /> |[[File:brain_section.jpg|thumb|280px|Brain BCC mesh cross-section]]<br /> |[[File:nidus_section.jpg|thumb|280px|Nidus BCC mesh cross-section]]<br /> |[[File:ventricles_section.jpg|thumb|280px|Ventricles BCC mesh cross-section]]<br /> |}<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Mesh Generation Parameters:'''<br /> ** '''Size:''' Controls the size of the mesh. The smaller the value the larger the mesh. Value should be between [1,20] (default: 8).<br /> ** '''Fidelity:''' Controls the subdivision of the elements that belong to more than one image labels. The larger the value the better the conformity of the mesh on the image label boundaries. Value should be between [0.1,1] (default: 0.8).<br /> ** '''Resample Resolution:''' Controls the image resampling. Suggested value is 0 (no-resampling) for large tissues and 1 or 2 for smaller tissues. Value should be 0 or 1 or 2 (default: 0).<br /> * '''Input/Output:'''<br /> ** '''Input Labeled Image:''' The input labeled image.<br /> ** '''Output Mesh File:''' The output tetrahedral mesh in vtk file format. (default: outputMesh.vtk)<br /> |[[Image:BCCPanel.jpg|thumb|320px|User Interface]]<br /> |}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/MeshCompression]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions&diff=38456 Documentation/Nightly/Extensions 2014-06-26T21:56:24Z <p>Fdrakopo: /* Cat 2 */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;noinclude&gt;<br /> __TOC__<br /> &lt;/noinclude&gt;= Extensions by Category =<br /> <br /> ==Cat 1==<br /> <br /> ==Cat 2==<br /> *[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )<br /> * [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)<br /> * [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)<br /> * [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)<br /> * [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroImport|DICOM-SRO import]] --&gt;<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroExport|DICOM-SRO export]] --&gt;<br /> ** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy (integrated into Slicer trunk)]]<br /> ** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)<br /> ** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)<br /> ** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)<br /> ** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)<br /> * [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)<br /> * [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)<br /> * [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)<br /> * [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)<br /> * [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)<br /> * [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)<br /> ** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]<br /> * [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]<br /> * [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)<br /> * [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)<br /> * [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)<br /> * [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)<br /> **[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)<br /> * [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]<br /> ** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]<br /> ** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]<br /> * [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)<br /> * [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)<br /> * [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)<br /> * [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]<br /> * [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]] (Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion | CBC 3D I2MConversion]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)<br /> ** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> ** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz and Nikos Chrisochoides)<br /> <br /> ==Cat 3==<br /> * [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation-&gt;TrainModel]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation-&gt;PredictLesions]] (Mark Scully)<br /> * [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)<br /> * [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)<br /> &lt;noinclude&gt;<br /> {{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}<br /> &lt;/noinclude&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions&diff=38455 Documentation/Nightly/Extensions 2014-06-26T21:56:02Z <p>Fdrakopo: /* Cat 2 */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;noinclude&gt;<br /> __TOC__<br /> &lt;/noinclude&gt;= Extensions by Category =<br /> <br /> ==Cat 1==<br /> <br /> ==Cat 2==<br /> *[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )<br /> * [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)<br /> * [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)<br /> * [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)<br /> * [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroImport|DICOM-SRO import]] --&gt;<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroExport|DICOM-SRO export]] --&gt;<br /> ** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy (integrated into Slicer trunk)]]<br /> ** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)<br /> ** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)<br /> ** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)<br /> ** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)<br /> * [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)<br /> * [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)<br /> * [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)<br /> * [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)<br /> * [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)<br /> * [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)<br /> ** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]<br /> * [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]<br /> * [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)<br /> * [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)<br /> * [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)<br /> * [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)<br /> **[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)<br /> * [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]<br /> ** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]<br /> ** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]<br /> * [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)<br /> * [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)<br /> * [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)<br /> * [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]<br /> * [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]] (Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/CBC\_3D\_I2MConversion | CBC 3D I2MConversion]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)<br /> ** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> ** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz and Nikos Chrisochoides)<br /> <br /> ==Cat 3==<br /> * [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation-&gt;TrainModel]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation-&gt;PredictLesions]] (Mark Scully)<br /> * [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)<br /> * [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)<br /> &lt;noinclude&gt;<br /> {{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}<br /> &lt;/noinclude&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/MeshCompression&diff=38454 Documentation/Nightly/Modules/MeshCompression 2014-06-26T21:54:14Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion |CBC_3D_I2MConversion]]&lt;br&gt;<br /> Acknowledgments:<br /> *This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.<br /> <br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The Mesh Compression (MC) module deforms the input tetrahedral mesh towards the boundaries of the input labeled image. Two point sets are extracted for the mesh deformation. The first (source point set) consists of the surface vertices in the input mesh. The second (target point set) consists of the surface edge points in the input labeled image. After the extraction of the two point sets, the input mesh is deformed by registering the source to the target point set using a Physics-Based Non-Rigid Registration method. The current version of the module supports a single-tissue labeled image and mesh.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[File:brain_before.jpg|thumb|300px|Brain BCC mesh before MC]]<br /> |[[File:brain_after.jpg|thumb|300px|Brain BCC mesh after MC]]<br /> |[[File:brain_after_section.jpg|thumb|300px|Brain BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:nidus_before.jpg|thumb|300px|Nidus BCC mesh before MC]]<br /> |[[File:nidus_after.jpg|thumb|300px|Nidus BCC mesh after MC]]&lt;br&gt;<br /> |[[File:nidus_after_section.jpg|thumb|300px|Nidus BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:ventricles_before.jpg|thumb|300px|Ventricles BCC mesh before MC]]<br /> |[[File:ventricles_after.jpg|thumb|300px|Ventricles BCC mesh after MC]]<br /> |[[File:ventricles_after_section.jpg|thumb|300px|Ventricles BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:target_points.jpg|thumb|960px|How the non-connectivity parameter influences the number of the extracted target points]]<br /> |}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Mesh Compression Parameters:'''<br /> ** '''Flexibility:''' Controls the trade-off between the regularization energy defined by the stress energy of a linear bio-mechanical elastic model, and the similarity energy. Value should be between [0.1,1] (default: 1).<br /> ** '''Number of Iterations:''' Controls the number of iterations for the compressor. The larger the value the closer the boundaries of the input mesh to the boundaries of the input image. A large number of iterations might cause distorted poor-quality elements. Value should be between [1,10] (default: 3).<br /> ** '''Non Connectivity:''' Controls the density of the extracted target points via a prohibited connectivity between adjacent blocks of voxels. The larger the value the denser the target point set. 0 is vertex non-connectivity (26 neighbors), 1 is edge non-connectivity (18 neighbors), 2 is face non-connectivity (6 neighbors) and 3 is no non-connectivity. Value should be 0 or 1 or 2 or 3. (default: 0).<br /> * '''Input/Output:'''<br /> ** '''Input Labeled Image:''' The input labeled image.<br /> ** '''Input Mesh File:''' The input tetrahedral mesh in vtk file format.<br /> ** '''Output Mesh File:''' The output deformed mesh in vtk file format (optional) (default: deformedMesh.vtk).<br /> ** '''Output Source Points File:''' The extracted source points in vtk file format (optional). The source points are the surface vertices of the input mesh.<br /> ** '''Output Target Points File:''' The extracted target points in vtk file format (optional). The target points are the surface edge points of the input labeled image.<br /> ** '''Output Surface Triangles File:''' The extracted surface triangles of the input mesh in vtk file format (optional).<br /> |[[Image:MCPanel.jpg|thumb|380px|User Interface]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/BodyCentricCubicMesh]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/BodyCentricCubicMesh&diff=38453 Documentation/Nightly/Modules/BodyCentricCubicMesh 2014-06-26T21:53:51Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion |CBC_3D_I2MConversion]]&lt;br&gt;<br /> Acknowledgments:<br /> *This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.<br /> <br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu<br /> &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module generates a Body Centric Cubic (BCC) mesh from a labeled image. Initially the generated mesh is homogeneous, that means does not distinguish different tissues. Later the module specifies which tissue each tetrahedron belongs to. Each tissue is capable of automatically adjusting its resolution based on its geometric complexity and the predefined subdivision criterion. The current version of the module supports a single-tissue input labeled image.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[File:brain.jpg|thumb|280px|Brain BCC mesh]]<br /> |[[File:nidus.jpg|thumb|280px|Nidus BCC mesh]]<br /> |[[File:ventricles.jpg|thumb|280px|Ventricles BCC mesh]]<br /> |}<br /> {|<br /> |[[File:brain_section.jpg|thumb|280px|Brain BCC mesh cross-section]]<br /> |[[File:nidus_section.jpg|thumb|280px|Nidus BCC mesh cross-section]]<br /> |[[File:ventricles_section.jpg|thumb|280px|Ventricles BCC mesh cross-section]]<br /> |}<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Mesh Generation Parameters:'''<br /> ** '''Size:''' Controls the size of the mesh. The smaller the value the larger the mesh. Value should be between [1,20] (default: 8).<br /> ** '''Fidelity:''' Controls the subdivision of the elements that belong to more than one image labels. The larger the value the better the conformity of the mesh on the image label boundaries. Value should be between [0.1,1] (default: 0.8).<br /> ** '''Resample Resolution:''' Controls the image resampling. Suggested value is 0 (no-resampling) for large tissues and 1 or 2 for smaller tissues. Value should be 0 or 1 or 2 (default: 0).<br /> * '''Input/Output:'''<br /> ** '''Input Labeled Image:''' The input labeled image.<br /> ** '''Output Mesh File:''' The output tetrahedral mesh in vtk file format. (default: outputMesh.vtk)<br /> |[[Image:BCCPanel.jpg|thumb|320px|User Interface]]<br /> |}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/MeshCompression]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions&diff=38452 Documentation/Nightly/Extensions 2014-06-26T21:52:53Z <p>Fdrakopo: /* Cat 2 */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;noinclude&gt;<br /> __TOC__<br /> &lt;/noinclude&gt;= Extensions by Category =<br /> <br /> ==Cat 1==<br /> <br /> ==Cat 2==<br /> *[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )<br /> * [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)<br /> * [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)<br /> * [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)<br /> * [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroImport|DICOM-SRO import]] --&gt;<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroExport|DICOM-SRO export]] --&gt;<br /> ** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy (integrated into Slicer trunk)]]<br /> ** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)<br /> ** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)<br /> ** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)<br /> ** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)<br /> * [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)<br /> * [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)<br /> * [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)<br /> * [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)<br /> * [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)<br /> * [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)<br /> ** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]<br /> * [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]<br /> * [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)<br /> * [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)<br /> * [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)<br /> * [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)<br /> **[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)<br /> * [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]<br /> ** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]<br /> ** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]<br /> * [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)<br /> * [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)<br /> * [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)<br /> * [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]<br /> * [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]] (Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion | CBC 3D I2MConversion]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)<br /> ** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> ** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz and Nikos Chrisochoides)<br /> <br /> ==Cat 3==<br /> * [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation-&gt;TrainModel]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation-&gt;PredictLesions]] (Mark Scully)<br /> * [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)<br /> * [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)<br /> &lt;noinclude&gt;<br /> {{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}<br /> &lt;/noinclude&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions&diff=38450 Documentation/Nightly/Extensions 2014-06-26T21:49:03Z <p>Fdrakopo: /* Cat 2 */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;noinclude&gt;<br /> __TOC__<br /> &lt;/noinclude&gt;= Extensions by Category =<br /> <br /> ==Cat 1==<br /> <br /> ==Cat 2==<br /> *[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )<br /> * [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)<br /> * [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)<br /> * [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)<br /> * [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroImport|DICOM-SRO import]] --&gt;<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroExport|DICOM-SRO export]] --&gt;<br /> ** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy (integrated into Slicer trunk)]]<br /> ** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)<br /> ** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)<br /> ** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)<br /> ** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)<br /> * [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)<br /> * [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)<br /> * [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)<br /> * [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)<br /> * [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)<br /> * [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)<br /> ** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]<br /> * [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]<br /> * [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)<br /> * [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)<br /> * [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)<br /> * [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)<br /> **[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)<br /> * [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]<br /> ** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]<br /> ** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]<br /> * [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)<br /> * [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)<br /> * [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)<br /> * [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]<br /> * [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]] (Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion | CBC_3D_I2MConversion]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)<br /> ** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> ** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz and Nikos Chrisochoides)<br /> <br /> ==Cat 3==<br /> * [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation-&gt;TrainModel]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation-&gt;PredictLesions]] (Mark Scully)<br /> * [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)<br /> * [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)<br /> &lt;noinclude&gt;<br /> {{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}<br /> &lt;/noinclude&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/MeshCompression&diff=38446 Documentation/Nightly/Modules/MeshCompression 2014-06-26T18:54:12Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/CBC3DI2MConversion |CBC3DI2MConversion]]&lt;br&gt;<br /> Acknowledgments:<br /> *This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.<br /> <br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The Mesh Compression (MC) module deforms the input tetrahedral mesh towards the boundaries of the input labeled image. Two point sets are extracted for the mesh deformation. The first (source point set) consists of the surface vertices in the input mesh. The second (target point set) consists of the surface edge points in the input labeled image. After the extraction of the two point sets, the input mesh is deformed by registering the source to the target point set using a Physics-Based Non-Rigid Registration method. The current version of the module supports a single-tissue labeled image and mesh.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[File:brain_before.jpg|thumb|300px|Brain BCC mesh before MC]]<br /> |[[File:brain_after.jpg|thumb|300px|Brain BCC mesh after MC]]<br /> |[[File:brain_after_section.jpg|thumb|300px|Brain BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:nidus_before.jpg|thumb|300px|Nidus BCC mesh before MC]]<br /> |[[File:nidus_after.jpg|thumb|300px|Nidus BCC mesh after MC]]&lt;br&gt;<br /> |[[File:nidus_after_section.jpg|thumb|300px|Nidus BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:ventricles_before.jpg|thumb|300px|Ventricles BCC mesh before MC]]<br /> |[[File:ventricles_after.jpg|thumb|300px|Ventricles BCC mesh after MC]]<br /> |[[File:ventricles_after_section.jpg|thumb|300px|Ventricles BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:target_points.jpg|thumb|960px|How the non-connectivity parameter influences the number of the extracted target points]]<br /> |}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Mesh Compression Parameters:'''<br /> ** '''Flexibility:''' Controls the trade-off between the regularization energy defined by the stress energy of a linear bio-mechanical elastic model, and the similarity energy. Value should be between [0.1,1] (default: 1).<br /> ** '''Number of Iterations:''' Controls the number of iterations for the compressor. The larger the value the closer the boundaries of the input mesh to the boundaries of the input image. A large number of iterations might cause distorted poor-quality elements. Value should be between [1,10] (default: 3).<br /> ** '''Non Connectivity:''' Controls the density of the extracted target points via a prohibited connectivity between adjacent blocks of voxels. The larger the value the denser the target point set. 0 is vertex non-connectivity (26 neighbors), 1 is edge non-connectivity (18 neighbors), 2 is face non-connectivity (6 neighbors) and 3 is no non-connectivity. Value should be 0 or 1 or 2 or 3. (default: 0).<br /> * '''Input/Output:'''<br /> ** '''Input Labeled Image:''' The input labeled image.<br /> ** '''Input Mesh File:''' The input tetrahedral mesh in vtk file format.<br /> ** '''Output Mesh File:''' The output deformed mesh in vtk file format (optional) (default: deformedMesh.vtk).<br /> ** '''Output Source Points File:''' The extracted source points in vtk file format (optional). The source points are the surface vertices of the input mesh.<br /> ** '''Output Target Points File:''' The extracted target points in vtk file format (optional). The target points are the surface edge points of the input labeled image.<br /> ** '''Output Surface Triangles File:''' The extracted surface triangles of the input mesh in vtk file format (optional).<br /> |[[Image:MCPanel.jpg|thumb|380px|User Interface]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/BodyCentricCubicMesh]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/BodyCentricCubicMesh&diff=38445 Documentation/Nightly/Modules/BodyCentricCubicMesh 2014-06-26T18:53:51Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/CBC3DI2MConversion |CBC3DI2MConversion]]&lt;br&gt;<br /> Acknowledgments:<br /> *This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.<br /> <br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu<br /> &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module generates a Body Centric Cubic (BCC) mesh from a labeled image. Initially the generated mesh is homogeneous, that means does not distinguish different tissues. Later the module specifies which tissue each tetrahedron belongs to. Each tissue is capable of automatically adjusting its resolution based on its geometric complexity and the predefined subdivision criterion. The current version of the module supports a single-tissue input labeled image.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[File:brain.jpg|thumb|280px|Brain BCC mesh]]<br /> |[[File:nidus.jpg|thumb|280px|Nidus BCC mesh]]<br /> |[[File:ventricles.jpg|thumb|280px|Ventricles BCC mesh]]<br /> |}<br /> {|<br /> |[[File:brain_section.jpg|thumb|280px|Brain BCC mesh cross-section]]<br /> |[[File:nidus_section.jpg|thumb|280px|Nidus BCC mesh cross-section]]<br /> |[[File:ventricles_section.jpg|thumb|280px|Ventricles BCC mesh cross-section]]<br /> |}<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Mesh Generation Parameters:'''<br /> ** '''Size:''' Controls the size of the mesh. The smaller the value the larger the mesh. Value should be between [1,20] (default: 8).<br /> ** '''Fidelity:''' Controls the subdivision of the elements that belong to more than one image labels. The larger the value the better the conformity of the mesh on the image label boundaries. Value should be between [0.1,1] (default: 0.8).<br /> ** '''Resample Resolution:''' Controls the image resampling. Suggested value is 0 (no-resampling) for large tissues and 1 or 2 for smaller tissues. Value should be 0 or 1 or 2 (default: 0).<br /> * '''Input/Output:'''<br /> ** '''Input Labeled Image:''' The input labeled image.<br /> ** '''Output Mesh File:''' The output tetrahedral mesh in vtk file format. (default: outputMesh.vtk)<br /> |[[Image:BCCPanel.jpg|thumb|320px|User Interface]]<br /> |}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/MeshCompression]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions&diff=38444 Documentation/Nightly/Extensions 2014-06-26T18:51:15Z <p>Fdrakopo: /* Cat 2 */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;noinclude&gt;<br /> __TOC__<br /> &lt;/noinclude&gt;= Extensions by Category =<br /> <br /> ==Cat 1==<br /> <br /> ==Cat 2==<br /> *[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )<br /> * [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)<br /> * [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)<br /> * [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)<br /> * [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)<br /> * [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br /> ** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br /> ** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroImport|DICOM-SRO import]] --&gt;<br /> &lt;!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroExport|DICOM-SRO export]] --&gt;<br /> ** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy (integrated into Slicer trunk)]]<br /> ** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]<br /> *** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]<br /> * [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)<br /> ** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)<br /> ** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)<br /> ** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)<br /> ** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)<br /> * [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)<br /> * [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)<br /> * [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)<br /> * [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)<br /> * [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)<br /> * [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br /> * [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)<br /> * [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)<br /> ** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]<br /> * [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]<br /> * [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)<br /> * [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)<br /> * [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)<br /> * [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)<br /> * [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)<br /> * [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)<br /> **[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)<br /> * [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)<br /> * [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)<br /> * [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)<br /> ** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]<br /> ** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]<br /> ** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]<br /> * [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)<br /> * [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)<br /> * [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)<br /> * [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)<br /> * [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)<br /> * [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)<br /> * [[Documentation/{{documentation/version}}/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]<br /> ** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]<br /> * [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]] (Junichi Tokuda)<br /> * [[Documentation/{{documentation/version}}/Extensions/CBC3DI2MConversion | CBC3DI2MConversion]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)<br /> ** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> ** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> * [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz and Nikos Chrisochoides)<br /> <br /> ==Cat 3==<br /> * [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation-&gt;TrainModel]] (Mark Scully)<br /> **[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation-&gt;PredictLesions]] (Mark Scully)<br /> * [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)<br /> * [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)<br /> &lt;noinclude&gt;<br /> {{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}<br /> &lt;/noinclude&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CBC_3D_I2MConversion&diff=38442 Documentation/Nightly/Extensions/CBC 3D I2MConversion 2014-06-26T18:47:17Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/CBC3DI2MConversion | CBC3DI2MConversion]]&lt;br&gt;<br /> Acknowledgments:<br /> This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> CBC3DI2MConversion is a software for generating high quality tetrahedral meshes from brain labeled images.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> *[[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Use Cases}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br /> N/A<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/extension-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=File:I2M_logo.jpg&diff=38424 File:I2M logo.jpg 2014-06-25T21:20:22Z <p>Fdrakopo: uploaded a new version of &quot;File:I2M logo.jpg&quot;</p> <hr /> <div></div> Fdrakopo https://www.slicer.org/w/index.php?title=File:PBNRR_logo.jpg&diff=38423 File:PBNRR logo.jpg 2014-06-25T21:19:53Z <p>Fdrakopo: uploaded a new version of &quot;File:PBNRR logo.jpg&quot;</p> <hr /> <div></div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38387 Documentation/Nightly/Extensions/PBNRR 2014-06-24T17:46:34Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Registration Parameters:'''<br /> ** '''Block Radius:''' Radius (in image voxels) of the selected image blocks in each dimension (default: 1,1,1).<br /> ** '''Window Radius:''' Radius (in image voxels) of the Block Matching window in each dimension (default: 5,5,5).<br /> ** '''Selection Fraction:''' Fraction of the selected blocks from the total number of image blocks. Value should be between [0.01,1] (default: 0.05).<br /> ** '''Rejection Fraction:''' Fraction of the rejected blocks from the number of the selected image blocks. Value should be between [0.01,1) (default: 0.25).<br /> ** '''Outlier Rejection Steps:''' Number of outlier rejection steps. Value should be between [1,20] (default: 5).<br /> ** '''Interpolation Steps:''' Number of interpolation steps. Value should be between [1,20] (default: 5).<br /> ** '''Young Modulus:''' Young Modulus of the linear bio-mechanical model (default: 0.0021 N/mm2).<br /> ** '''Poisson Ratio:''' Poisson Ratio of the linear bio-mechanical model. Value should be between [0.10,0.49] (default: 0.45).<br /> <br /> * '''Input/Output:'''<br /> ** '''Input Moving Image:''' The input moving image.<br /> ** '''Input Fixed Image:''' The input moving image.<br /> ** '''Input Mask Image:''' The input moving image.<br /> ** '''Input Mesh:''' The input moving image.<br /> ** '''Output Volume:''' Moving image to the fixed image coordinate frame (optional).<br /> ** '''Output Direct Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the moving coordinate frame to the fixed coordinate frame (optional).<br /> ** '''Output Inverse Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the fixed coordinate frame to the moving coordinate frame (optional).<br /> ** '''Output Warped Mesh:''' The warped tetrahedral mesh in vtk file format (optional).<br /> |[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Olivier Clatz, Hervé Delingette, Ion-Florin Talos, Alexandra J. Golby, Ron Kikinis, Ferenc Jolesz, Nicholas Ayache, and Simon Warfield,“Robust Non-Rigid Registration to Capture Brain Shift from Intra-Operative MRI“, IEEE Transactions on Medical Imaging, 24(11):1417-1427, Nov. 2005. <br /> * Liu Y, Kot A, Drakopoulos F, Yao C, Fedorov A, Enquobahrie A, Clatz O and Chrisochoides NP (2014), ”An ITK implementation of a physics-based non-rigid registration method for brain deformation in image-guided neurosurgery”, Frontiers in Neuroinformatics 8:33. doi: 10.3389/fninf.2014.00033<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Registration]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=File:PBNRR_logo.jpg&diff=38386 File:PBNRR logo.jpg 2014-06-24T17:46:10Z <p>Fdrakopo: </p> <hr /> <div></div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38385 Documentation/Nightly/Extensions/PBNRR 2014-06-24T17:45:56Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> [[File:PBNRR_logo.jpg]]<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Registration Parameters:'''<br /> ** '''Block Radius:''' Radius (in image voxels) of the selected image blocks in each dimension (default: 1,1,1).<br /> ** '''Window Radius:''' Radius (in image voxels) of the Block Matching window in each dimension (default: 5,5,5).<br /> ** '''Selection Fraction:''' Fraction of the selected blocks from the total number of image blocks. Value should be between [0.01,1] (default: 0.05).<br /> ** '''Rejection Fraction:''' Fraction of the rejected blocks from the number of the selected image blocks. Value should be between [0.01,1) (default: 0.25).<br /> ** '''Outlier Rejection Steps:''' Number of outlier rejection steps. Value should be between [1,20] (default: 5).<br /> ** '''Interpolation Steps:''' Number of interpolation steps. Value should be between [1,20] (default: 5).<br /> ** '''Young Modulus:''' Young Modulus of the linear bio-mechanical model (default: 0.0021 N/mm2).<br /> ** '''Poisson Ratio:''' Poisson Ratio of the linear bio-mechanical model. Value should be between [0.10,0.49] (default: 0.45).<br /> <br /> * '''Input/Output:'''<br /> ** '''Input Moving Image:''' The input moving image.<br /> ** '''Input Fixed Image:''' The input moving image.<br /> ** '''Input Mask Image:''' The input moving image.<br /> ** '''Input Mesh:''' The input moving image.<br /> ** '''Output Volume:''' Moving image to the fixed image coordinate frame (optional).<br /> ** '''Output Direct Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the moving coordinate frame to the fixed coordinate frame (optional).<br /> ** '''Output Inverse Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the fixed coordinate frame to the moving coordinate frame (optional).<br /> ** '''Output Warped Mesh:''' The warped tetrahedral mesh in vtk file format (optional).<br /> |[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Olivier Clatz, Hervé Delingette, Ion-Florin Talos, Alexandra J. Golby, Ron Kikinis, Ferenc Jolesz, Nicholas Ayache, and Simon Warfield,“Robust Non-Rigid Registration to Capture Brain Shift from Intra-Operative MRI“, IEEE Transactions on Medical Imaging, 24(11):1417-1427, Nov. 2005. <br /> * Liu Y, Kot A, Drakopoulos F, Yao C, Fedorov A, Enquobahrie A, Clatz O and Chrisochoides NP (2014), ”An ITK implementation of a physics-based non-rigid registration method for brain deformation in image-guided neurosurgery”, Frontiers in Neuroinformatics 8:33. doi: 10.3389/fninf.2014.00033<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Registration]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CBC_3D_I2MConversion&diff=38383 Documentation/Nightly/Extensions/CBC 3D I2MConversion 2014-06-24T15:22:40Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/ImageToMeshConversion | Image-To-Mesh (I2M) Conversion]]&lt;br&gt;<br /> Acknowledgments:<br /> This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> Image-To-Mesh (I2M) Conversion is a software for generating high quality tetrahedral meshes from brain labeled images.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> *[[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Use Cases}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br /> N/A<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/extension-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CBC_3D_I2MConversion&diff=38382 Documentation/Nightly/Extensions/CBC 3D I2MConversion 2014-06-24T14:09:07Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/ImageToMeshConversion | Image-To-Mesh (I2M) Conversion]]&lt;br&gt;<br /> Acknowledgments:<br /> This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> Image-To-Mesh (I2M) Conversion is an open source software for generating high quality tetrahedral meshes from brain labeled images.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> *[[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Use Cases}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br /> N/A<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/extension-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CBC_3D_I2MConversion&diff=38381 Documentation/Nightly/Extensions/CBC 3D I2MConversion 2014-06-24T14:07:41Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/ImageToMeshConversion | Image-To-Mesh (I2M) Conversion]]&lt;br&gt;<br /> Acknowledgments:<br /> This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> [[File:I2M_logo.jpg]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> Image-To-Mesh (I2M) Conversion is an open source software for generating high quality tetrahedral meshes from brain labeled images.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> *[[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Use Cases}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br /> N/A<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/extension-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=File:I2M_logo.jpg&diff=38380 File:I2M logo.jpg 2014-06-24T14:07:02Z <p>Fdrakopo: </p> <hr /> <div></div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/MeshCompression&diff=38367 Documentation/Nightly/Modules/MeshCompression 2014-06-23T13:42:49Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/ImageToMeshConversion|Image-To-Mesh (I2M) Conversion]]&lt;br&gt;<br /> Acknowledgments:<br /> *This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.<br /> <br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The Mesh Compression (MC) module deforms the input tetrahedral mesh towards the boundaries of the input labeled image. Two point sets are extracted for the mesh deformation. The first (source point set) consists of the surface vertices in the input mesh. The second (target point set) consists of the surface edge points in the input labeled image. After the extraction of the two point sets, the input mesh is deformed by registering the source to the target point set using a Physics-Based Non-Rigid Registration method. The current version of the module supports a single-tissue labeled image and mesh.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[File:brain_before.jpg|thumb|300px|Brain BCC mesh before MC]]<br /> |[[File:brain_after.jpg|thumb|300px|Brain BCC mesh after MC]]<br /> |[[File:brain_after_section.jpg|thumb|300px|Brain BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:nidus_before.jpg|thumb|300px|Nidus BCC mesh before MC]]<br /> |[[File:nidus_after.jpg|thumb|300px|Nidus BCC mesh after MC]]&lt;br&gt;<br /> |[[File:nidus_after_section.jpg|thumb|300px|Nidus BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:ventricles_before.jpg|thumb|300px|Ventricles BCC mesh before MC]]<br /> |[[File:ventricles_after.jpg|thumb|300px|Ventricles BCC mesh after MC]]<br /> |[[File:ventricles_after_section.jpg|thumb|300px|Ventricles BCC mesh after MC (cross-section)]]<br /> |}<br /> <br /> {|<br /> |[[File:target_points.jpg|thumb|960px|How the non-connectivity parameter influences the number of the extracted target points]]<br /> |}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Mesh Compression Parameters:'''<br /> ** '''Flexibility:''' Controls the trade-off between the regularization energy defined by the stress energy of a linear bio-mechanical elastic model, and the similarity energy. Value should be between [0.1,1] (default: 1).<br /> ** '''Number of Iterations:''' Controls the number of iterations for the compressor. The larger the value the closer the boundaries of the input mesh to the boundaries of the input image. A large number of iterations might cause distorted poor-quality elements. Value should be between [1,10] (default: 3).<br /> ** '''Non Connectivity:''' Controls the density of the extracted target points via a prohibited connectivity between adjacent blocks of voxels. The larger the value the denser the target point set. 0 is vertex non-connectivity (26 neighbors), 1 is edge non-connectivity (18 neighbors), 2 is face non-connectivity (6 neighbors) and 3 is no non-connectivity. Value should be 0 or 1 or 2 or 3. (default: 0).<br /> * '''Input/Output:'''<br /> ** '''Input Labeled Image:''' The input labeled image.<br /> ** '''Input Mesh File:''' The input tetrahedral mesh in vtk file format.<br /> ** '''Output Mesh File:''' The output deformed mesh in vtk file format (optional) (default: deformedMesh.vtk).<br /> ** '''Output Source Points File:''' The extracted source points in vtk file format (optional). The source points are the surface vertices of the input mesh.<br /> ** '''Output Target Points File:''' The extracted target points in vtk file format (optional). The target points are the surface edge points of the input labeled image.<br /> ** '''Output Surface Triangles File:''' The extracted surface triangles of the input mesh in vtk file format (optional).<br /> |[[Image:MCPanel.jpg|thumb|380px|User Interface]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/BodyCentricCubicMesh]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/BodyCentricCubicMesh&diff=38366 Documentation/Nightly/Modules/BodyCentricCubicMesh 2014-06-23T13:42:23Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/ImageToMeshConversion|Image-To-Mesh (I2M) Conversion]]&lt;br&gt;<br /> Acknowledgments:<br /> *This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.<br /> <br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu<br /> &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module generates a Body Centric Cubic (BCC) mesh from a labeled image. Initially the generated mesh is homogeneous, that means does not distinguish different tissues. Later the module specifies which tissue each tetrahedron belongs to. Each tissue is capable of automatically adjusting its resolution based on its geometric complexity and the predefined subdivision criterion. The current version of the module supports a single-tissue input labeled image.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[File:brain.jpg|thumb|280px|Brain BCC mesh]]<br /> |[[File:nidus.jpg|thumb|280px|Nidus BCC mesh]]<br /> |[[File:ventricles.jpg|thumb|280px|Ventricles BCC mesh]]<br /> |}<br /> {|<br /> |[[File:brain_section.jpg|thumb|280px|Brain BCC mesh cross-section]]<br /> |[[File:nidus_section.jpg|thumb|280px|Nidus BCC mesh cross-section]]<br /> |[[File:ventricles_section.jpg|thumb|280px|Ventricles BCC mesh cross-section]]<br /> |}<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Mesh Generation Parameters:'''<br /> ** '''Size:''' Controls the size of the mesh. The smaller the value the larger the mesh. Value should be between [1,20] (default: 8).<br /> ** '''Fidelity:''' Controls the subdivision of the elements that belong to more than one image labels. The larger the value the better the conformity of the mesh on the image label boundaries. Value should be between [0.1,1] (default: 0.8).<br /> ** '''Resample Resolution:''' Controls the image resampling. Suggested value is 0 (no-resampling) for large tissues and 1 or 2 for smaller tissues. Value should be 0 or 1 or 2 (default: 0).<br /> * '''Input/Output:'''<br /> ** '''Input Labeled Image:''' The input labeled image.<br /> ** '''Output Mesh File:''' The output tetrahedral mesh in vtk file format. (default: outputMesh.vtk)<br /> |[[Image:BCCPanel.jpg|thumb|320px|User Interface]]<br /> |}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/MeshCompression]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38365 Documentation/Nightly/Extensions/PBNRR 2014-06-23T12:41:04Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Registration Parameters:'''<br /> ** '''Block Radius:''' Radius (in image voxels) of the selected image blocks in each dimension (default: 1,1,1).<br /> ** '''Window Radius:''' Radius (in image voxels) of the Block Matching window in each dimension (default: 5,5,5).<br /> ** '''Selection Fraction:''' Fraction of the selected blocks from the total number of image blocks. Value should be between [0.01,1] (default: 0.05).<br /> ** '''Rejection Fraction:''' Fraction of the rejected blocks from the number of the selected image blocks. Value should be between [0.01,1) (default: 0.25).<br /> ** '''Outlier Rejection Steps:''' Number of outlier rejection steps. Value should be between [1,20] (default: 5).<br /> ** '''Interpolation Steps:''' Number of interpolation steps. Value should be between [1,20] (default: 5).<br /> ** '''Young Modulus:''' Young Modulus of the linear bio-mechanical model (default: 0.0021 N/mm2).<br /> ** '''Poisson Ratio:''' Poisson Ratio of the linear bio-mechanical model. Value should be between [0.10,0.49] (default: 0.45).<br /> <br /> * '''Input/Output:'''<br /> ** '''Input Moving Image:''' The input moving image.<br /> ** '''Input Fixed Image:''' The input moving image.<br /> ** '''Input Mask Image:''' The input moving image.<br /> ** '''Input Mesh:''' The input moving image.<br /> ** '''Output Volume:''' Moving image to the fixed image coordinate frame (optional).<br /> ** '''Output Direct Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the moving coordinate frame to the fixed coordinate frame (optional).<br /> ** '''Output Inverse Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the fixed coordinate frame to the moving coordinate frame (optional).<br /> ** '''Output Warped Mesh:''' The warped tetrahedral mesh in vtk file format (optional).<br /> |[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Olivier Clatz, Hervé Delingette, Ion-Florin Talos, Alexandra J. Golby, Ron Kikinis, Ferenc Jolesz, Nicholas Ayache, and Simon Warfield,“Robust Non-Rigid Registration to Capture Brain Shift from Intra-Operative MRI“, IEEE Transactions on Medical Imaging, 24(11):1417-1427, Nov. 2005. <br /> * Liu Y, Kot A, Drakopoulos F, Yao C, Fedorov A, Enquobahrie A, Clatz O and Chrisochoides NP (2014), ”An ITK implementation of a physics-based non-rigid registration method for brain deformation in image-guided neurosurgery”, Frontiers in Neuroinformatics 8:33. doi: 10.3389/fninf.2014.00033<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Registration]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CBC_3D_I2MConversion&diff=38364 Documentation/Nightly/Extensions/CBC 3D I2MConversion 2014-06-23T12:40:39Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/ImageToMeshConversion | Image-To-Mesh (I2M) Conversion]]&lt;br&gt;<br /> Acknowledgments:<br /> This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> Image-To-Mesh (I2M) Conversion is an open source software for generating high quality tetrahedral meshes from brain labeled images.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> *[[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Use Cases}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br /> N/A<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/extension-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CBC_3D_I2MConversion&diff=38363 Documentation/Nightly/Extensions/CBC 3D I2MConversion 2014-06-23T12:40:25Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/ImageToMeshConversion | Image-To-Mesh (I2M) Conversion]]&lt;br&gt;<br /> Acknowledgments:<br /> This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu /&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Extension Description}}<br /> Image-To-Mesh (I2M) Conversion is an open source software for generating high quality tetrahedral meshes from brain labeled images.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Modules}}<br /> *[[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br /> *[[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Use Cases}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br /> N/A<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/extension-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/extension-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules&diff=38346 Documentation/Nightly/Modules 2014-06-20T22:39:24Z <p>Fdrakopo: /* Mesh Generation */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> =Modules by Category=<br /> ==Core Modules==<br /> <br /> {{documentation/{{documentation/version}}/Developers/random-image}}<br /> <br /> *[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)<br /> *[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)<br /> *[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br /> **[[Documentation/{{documentation/version}}/Modules/Editor/WatershedFromMarkers|WatershedFromMarkers]] (Bradley Lowekamp) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/Markups|Markups]] (Nicole Aucoin)<br /> *[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)<br /> *[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich) <br /> *[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) <br /> *[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)<br /> *[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)<br /> *[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)<br /> <br /> ==Wizards==<br /> <br /> ==Informatics==<br /> *[[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] (Charles Marion)<br /> *[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)<br /> <br /> ==Registration==<br /> *[[:Category:Documentation/{{documentation/version}}/Modules/Registration|Introduction to Registration]] (Dominik Meier)<br /> *[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)<br /> *[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)<br /> *Specialized<br /> **[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)<br /> **[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) {{wip}}<br /> **Vector Demon Registration (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)<br /> **[[Documentation/{{documentation/version}}/Modules/SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao) {{wip}}<br /> <br /> ==Segmentation==<br /> *[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) <br /> *[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) <br /> *[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan) <br /> *[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br /> *Specialized<br /> **[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)<br /> **[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)<br /> **[[Documentation/{{documentation/version}}/Modules/LAScarSegmenter|Left Atrial Scar Segmenter]] (Liangjia Zhu)<br /> **[[Documentation/{{documentation/version}}/Modules/LASegmenter|Left Atrium Segmenter]] (Liangjia Zhu)<br /> **[[Documentation/{{documentation/version}}/Modules/FastGrowCut|Fast GrowCut]] (Liangjia Zhu) {{wip}}<br /> <br /> ==Quantification==<br /> *[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)<br /> *[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)<br /> *[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)<br /> <br /> ==Diffusion== <br /> *DWI to Full Brain Tractography (Demian Wasserman) {{wip}}<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) {{wip}}<br /> *Tractography<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Interactive Seeding]] (Alex Yarmarkovich)<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]<br /> *Utilities<br /> **[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) {{wip}}<br /> *Data Conversion<br /> **[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]] {{wip}} (Sonia Pujol) <br /> **[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]] {{wip}} (Sonia Pujol)<br /> **[[Documentation/{{documentation/version}}/Modules/FiberBundleToLabelMap|Fiber Bundle to Label Map]] (Steve Pieper)<br /> <br /> ==IGT==<br /> *[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Extensions/SlicerIGT| SlicerIGT]] (Tamas Ungi, Junichi Tokuda) {{wip}}<br /> <br /> ==Filtering==<br /> *[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)<br /> *[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) <br /> *[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/SimpleFilters|Simple Filters]] (Bradley Lowekamp) {{wip}}<br /> *Arithmetic <br /> **[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin) <br /> **[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin) <br /> **[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) {{wip}}<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) {{wip}} <br /> **[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) {{wip}}<br /> *Morphology<br /> **[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)<br /> **[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (Jim Miller) {{wip}}<br /> <br /> ==Surface Models==<br /> *[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/SurfaceToolbox| SurfaceToolbox]] (Luca Antiga)<br /> <br /> ==Converters==<br /> *[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)<br /> *[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) <br /> *[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller) <br /> *[[Documentation/{{documentation/version}}/Modules/VectorToScalarVolume| Vector to Scalar Volume]] (Steve Pieper) <br /> {{wip}}<br /> <br /> ==Endoscopy==<br /> *[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br /> <br /> =={{wip}} Work in Progress {{wip}}==<br /> * MultiVolume Support<br /> **[[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultiVolume Importer]] (Andrey Fedorov)<br /> **[[Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (Andrey Fedorov)<br /> <br /> ==Developer Tools==<br /> *[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ExtensionWizard |Extension Wizard]] (Matthew Woehlke) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)<br /> *Performance Tests<br /> *Tractography<br /> <br /> ==Legacy==<br /> *Converters<br /> **[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]]<br /> *Diffusion<br /> **Denoising<br /> ***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]<br /> *Filtering<br /> **[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) {{wip}}<br /> *Registration<br /> **[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett){{wip}}<br /> &lt;!--<br /> **[[Documentation/{{documentation/version}}/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] {{wip}}<br /> --&gt;<br /> *Segmentation<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) {{wip}}</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly&diff=38345 Documentation/Nightly 2014-06-20T22:39:06Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> __NOTOC__<br /> {{documentation/versionlist}}<br /> <br /> {| border=&quot;0&quot; align=&quot;center&quot; width=&quot;100%&quot; valign=&quot;top&quot; cellspacing=&quot;7&quot; cellpadding=&quot;2&quot;<br /> |-<br /> ! width=&quot;33%&quot;|<br /> ! |<br /> ! width=&quot;33%&quot;|<br /> ! |<br /> ! width=&quot;33%&quot;|<br /> |- <br /> |valign=&quot;top&quot;|<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Where to start ?&lt;/span&gt;<br /> ----<br /> * [[Documentation/{{documentation/version}}/Training|Training pages]]<br /> : Information on how to use Slicer {{documentation/version}}<br /> <br /> * [[Documentation/{{documentation/version}}/FAQ|FAQ]]<br /> : Set of common questions/answers<br /> * [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Users mailing list] / [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Sign-up] / [http://slicer-users.65878.n3.nabble.com/ Browse archives]<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;How to&lt;/span&gt;<br /> ----<br /> * [[Documentation/{{documentation/version}}/Report a problem|Report a problem]] / [[Documentation/{{documentation/version}}/Create_a_feature_request|Create a feature request]]{{new}}<br /> ----<br /> {{:{{FULLPAGENAME}}/SlicerApplication}}<br /> <br /> |bgcolor=&quot;#CCCCCC&quot;|<br /> |valign=&quot;top&quot;|<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Module Categories&lt;/span&gt;<br /> ----<br /> * [[#Core Modules|Core Modules]]<br /> * [[#Wizards|Wizards]]<br /> * [[#Informatics|Informatics]]<br /> * [[#Registration|Registration]]<br /> * [[#Segmentation|Segmentation]]<br /> * [[#Quantification|Quantification]]<br /> * [[#Diffusion|Diffusion]]<br /> * [[#IGT|IGT]]<br /> * [[#Filtering|Filtering]]<br /> * [[#Surface Models|Surface Models]]<br /> * [[#Converters|Converters]]<br /> * [[#Endoscopy|Endoscopy]]<br /> * [[#Work in Progress| Work in Progress]]<br /> * [[#Developer Tools|Developer Tools]]<br /> * [[#Legacy|Legacy]]<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Extension Categories&lt;/span&gt; {{new}}<br /> ----<br /> {{note}} What are these categories ? See [[Documentation/{{documentation/version}}/Extensions/CatalogPolicies|here]]<br /> <br /> * [[#Cat_1|Category 1]]<br /> * [[#Cat_2|Category 2]]<br /> * [[#Cat_3|Category 3]]<br /> <br /> |bgcolor=&quot;#CCCCCC&quot;|<br /> |valign=&quot;top&quot;|<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Developers Corner&lt;/span&gt;<br /> ----<br /> * [[Documentation/{{documentation/version}}/Developers | Information for Software Developers]]{{updated}}<br /> : Source code, contribute patch, develop modules<br /> <br /> * [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Developers mailing list] / [http://slicer-devel.65872.n3.nabble.com/ Browse archives]<br /> : Intended for discussion of programming related questions<br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Miscellaneous&lt;/span&gt;<br /> ----<br /> &lt;!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --&gt;<br /> <br /> * [[Documentation/{{documentation/version}}/HowTo|Documentation guidelines]]<br /> : Slicer user documentation principle and guidelines<br /> <br /> * [[Slicer4:VisualBlog|Visual blog]]<br /> : Set of screenshots showing Slicer in action.<br /> <br /> * [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]<br /> : Platform specific issues and considerations<br /> <br /> * [[Documentation/{{documentation/version}}/Announcements|Announcements]] &amp; [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]<br /> <br /> * [http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable Slicer Registration Case Library]<br /> : Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself. <br /> <br /> ----<br /> &lt;span style=&quot;color: #555555; font-size: 18px; font-weight: bold;&quot;&gt;Documentación en Español&lt;/span&gt; {{new}}<br /> ----<br /> * [http://robustiana.com/156-intro-a-3d-slicer Introducción a 3D Slicer en Español]<br /> : Breve descripción de proyecto y un breve viaje por sus principales herramientas y funcionalidades. <br /> <br /> * [http://robustiana.com/157-recon-volumetricas Reconstrucciones volumétricas con 3D Slicer]<br /> : Guía de uso para la herramienta de creación de reconstrucciones volumétricas de 3D Slicer. <br /> <br /> * [http://robustiana.com/158-contornos-3d-slicer Crear modelos/contornos de órganos con 3D Slicer]<br /> : Guía rápida introductoria para la creación de contornos de órganos para generar vistas volumétricas.<br /> <br /> * [http://robustiana.com/159-endoscopias-3d-slicer Endoscopías virtuales con 3D Slicer]<br /> : Manual de uso de la herramienta para 3D Slicer desarrollada por Steve Pieper para realizar endoscopías virtuales. <br /> <br /> * [http://robustiana.com/163-rt-slicer-3d Creando curvas de isodosis con SlicerRT de 3D Slicer]<br /> : Introducción a la extensión SlicerRT para 3D Slicer enfocada en investigación en radioterapia. <br /> <br /> |}<br /> <br /> {{:{{FULLPAGENAME}}/Modules}}<br /> <br /> {{:{{FULLPAGENAME}}/Extensions}}</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules&diff=38344 Documentation/Nightly/Modules 2014-06-20T18:56:25Z <p>Fdrakopo: /* Registration */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> =Modules by Category=<br /> ==Core Modules==<br /> <br /> {{documentation/{{documentation/version}}/Developers/random-image}}<br /> <br /> *[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)<br /> *[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)<br /> *[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br /> **[[Documentation/{{documentation/version}}/Modules/Editor/WatershedFromMarkers|WatershedFromMarkers]] (Bradley Lowekamp) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/Markups|Markups]] (Nicole Aucoin)<br /> *[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)<br /> *[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich) <br /> *[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) <br /> *[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)<br /> *[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)<br /> *[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)<br /> <br /> ==Wizards==<br /> <br /> ==Informatics==<br /> *[[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] (Charles Marion)<br /> *[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)<br /> <br /> ==Registration==<br /> *[[:Category:Documentation/{{documentation/version}}/Modules/Registration|Introduction to Registration]] (Dominik Meier)<br /> *[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)<br /> *[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)<br /> *Specialized<br /> **[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)<br /> **[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) {{wip}}<br /> **Vector Demon Registration (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)<br /> **[[Documentation/{{documentation/version}}/Modules/SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao) {{wip}}<br /> <br /> ==Segmentation==<br /> *[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) <br /> *[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) <br /> *[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan) <br /> *[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br /> *Specialized<br /> **[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)<br /> **[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)<br /> **[[Documentation/{{documentation/version}}/Modules/LAScarSegmenter|Left Atrial Scar Segmenter]] (Liangjia Zhu)<br /> **[[Documentation/{{documentation/version}}/Modules/LASegmenter|Left Atrium Segmenter]] (Liangjia Zhu)<br /> **[[Documentation/{{documentation/version}}/Modules/FastGrowCut|Fast GrowCut]] (Liangjia Zhu) {{wip}}<br /> <br /> ==Mesh Generation==<br /> * Image-To-Mesh (I2M) Conversion<br /> ** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)<br /> ** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)<br /> <br /> ==Quantification==<br /> *[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)<br /> *[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)<br /> *[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)<br /> <br /> ==Diffusion== <br /> *DWI to Full Brain Tractography (Demian Wasserman) {{wip}}<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) {{wip}}<br /> *Tractography<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Interactive Seeding]] (Alex Yarmarkovich)<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]<br /> *Utilities<br /> **[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) {{wip}}<br /> *Data Conversion<br /> **[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]] {{wip}} (Sonia Pujol) <br /> **[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]] {{wip}} (Sonia Pujol)<br /> **[[Documentation/{{documentation/version}}/Modules/FiberBundleToLabelMap|Fiber Bundle to Label Map]] (Steve Pieper)<br /> <br /> ==IGT==<br /> *[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Extensions/SlicerIGT| SlicerIGT]] (Tamas Ungi, Junichi Tokuda) {{wip}}<br /> <br /> ==Filtering==<br /> *[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)<br /> *[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) <br /> *[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/SimpleFilters|Simple Filters]] (Bradley Lowekamp) {{wip}}<br /> *Arithmetic <br /> **[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin) <br /> **[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin) <br /> **[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) {{wip}}<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) {{wip}} <br /> **[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) {{wip}}<br /> *Morphology<br /> **[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)<br /> **[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (Jim Miller) {{wip}}<br /> <br /> ==Surface Models==<br /> *[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/SurfaceToolbox| SurfaceToolbox]] (Luca Antiga)<br /> <br /> ==Converters==<br /> *[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)<br /> *[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) <br /> *[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller) <br /> *[[Documentation/{{documentation/version}}/Modules/VectorToScalarVolume| Vector to Scalar Volume]] (Steve Pieper) <br /> {{wip}}<br /> <br /> ==Endoscopy==<br /> *[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br /> <br /> =={{wip}} Work in Progress {{wip}}==<br /> * MultiVolume Support<br /> **[[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultiVolume Importer]] (Andrey Fedorov)<br /> **[[Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (Andrey Fedorov)<br /> <br /> ==Developer Tools==<br /> *[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ExtensionWizard |Extension Wizard]] (Matthew Woehlke) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)<br /> *Performance Tests<br /> *Tractography<br /> <br /> ==Legacy==<br /> *Converters<br /> **[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]]<br /> *Diffusion<br /> **Denoising<br /> ***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]<br /> *Filtering<br /> **[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) {{wip}}<br /> *Registration<br /> **[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett){{wip}}<br /> &lt;!--<br /> **[[Documentation/{{documentation/version}}/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] {{wip}}<br /> --&gt;<br /> *Segmentation<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) {{wip}}</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules&diff=38343 Documentation/Nightly/Modules 2014-06-20T18:55:51Z <p>Fdrakopo: /* Registration */</p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> =Modules by Category=<br /> ==Core Modules==<br /> <br /> {{documentation/{{documentation/version}}/Developers/random-image}}<br /> <br /> *[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)<br /> *[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)<br /> *[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br /> **[[Documentation/{{documentation/version}}/Modules/Editor/WatershedFromMarkers|WatershedFromMarkers]] (Bradley Lowekamp) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/Markups|Markups]] (Nicole Aucoin)<br /> *[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)<br /> *[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich) <br /> *[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) <br /> *[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)<br /> *[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)<br /> *[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)<br /> <br /> ==Wizards==<br /> <br /> ==Informatics==<br /> *[[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] (Charles Marion)<br /> *[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)<br /> <br /> ==Registration==<br /> *[[:Category:Documentation/{{documentation/version}}/Modules/Registration|Introduction to Registration]] (Dominik Meier)<br /> *[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson)<br /> *[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson)<br /> *[[Documentation/{{documentation/version}}/Modules/PBNRR| Physics-Based Non-Rigid Registration]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz, Nikos Chrisochoides )<br /> *Specialized<br /> **[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)<br /> **[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) {{wip}}<br /> **Vector Demon Registration (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)<br /> **[[Documentation/{{documentation/version}}/Modules/SegmentationAidedRegistration|Segmentation Aided Registration]] (Yi Gao) {{wip}}<br /> <br /> ==Segmentation==<br /> *[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) <br /> *[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) <br /> *[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan) <br /> *[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br /> *Specialized<br /> **[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)<br /> **[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao)<br /> **[[Documentation/{{documentation/version}}/Modules/LAScarSegmenter|Left Atrial Scar Segmenter]] (Liangjia Zhu)<br /> **[[Documentation/{{documentation/version}}/Modules/LASegmenter|Left Atrium Segmenter]] (Liangjia Zhu)<br /> **[[Documentation/{{documentation/version}}/Modules/FastGrowCut|Fast GrowCut]] (Liangjia Zhu) {{wip}}<br /> <br /> ==Mesh Generation==<br /> * Image-To-Mesh (I2M) Conversion<br /> ** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)<br /> ** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)<br /> <br /> ==Quantification==<br /> *[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)<br /> *[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)<br /> *[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin)<br /> <br /> ==Diffusion== <br /> *DWI to Full Brain Tractography (Demian Wasserman) {{wip}}<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) {{wip}}<br /> *Tractography<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Interactive Seeding]] (Alex Yarmarkovich)<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]<br /> *Utilities<br /> **[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) {{wip}}<br /> *Data Conversion<br /> **[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]] {{wip}} (Sonia Pujol) <br /> **[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]] {{wip}} (Sonia Pujol)<br /> **[[Documentation/{{documentation/version}}/Modules/FiberBundleToLabelMap|Fiber Bundle to Label Map]] (Steve Pieper)<br /> <br /> ==IGT==<br /> *[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Extensions/SlicerIGT| SlicerIGT]] (Tamas Ungi, Junichi Tokuda) {{wip}}<br /> <br /> ==Filtering==<br /> *[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)<br /> *[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) <br /> *[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/SimpleFilters|Simple Filters]] (Bradley Lowekamp) {{wip}}<br /> *Arithmetic <br /> **[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin) <br /> **[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin) <br /> **[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) {{wip}}<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) {{wip}} <br /> **[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) {{wip}}<br /> *Morphology<br /> **[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller)<br /> **[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak Image Filter]] (Jim Miller) {{wip}}<br /> <br /> ==Surface Models==<br /> *[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin) <br /> *[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/SurfaceToolbox| SurfaceToolbox]] (Luca Antiga)<br /> <br /> ==Converters==<br /> *[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)<br /> *[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) <br /> *[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller) <br /> *[[Documentation/{{documentation/version}}/Modules/VectorToScalarVolume| Vector to Scalar Volume]] (Steve Pieper) <br /> {{wip}}<br /> <br /> ==Endoscopy==<br /> *[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br /> <br /> =={{wip}} Work in Progress {{wip}}==<br /> * MultiVolume Support<br /> **[[Documentation/{{documentation/version}}/Modules/MultiVolumeImporter|MultiVolume Importer]] (Andrey Fedorov)<br /> **[[Documentation/{{documentation/version}}/Modules/MultiVolumeExplorer|MultiVolume Explorer]] (Andrey Fedorov)<br /> <br /> ==Developer Tools==<br /> *[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/ExtensionWizard |Extension Wizard]] (Matthew Woehlke) {{wip}}<br /> *[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin)<br /> *Performance Tests<br /> *Tractography<br /> <br /> ==Legacy==<br /> *Converters<br /> **[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]]<br /> *Diffusion<br /> **Denoising<br /> ***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]]<br /> *Filtering<br /> **[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) {{wip}}<br /> *Registration<br /> **[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett){{wip}}<br /> &lt;!--<br /> **[[Documentation/{{documentation/version}}/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] {{wip}}<br /> --&gt;<br /> *Segmentation<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) {{wip}}</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/BodyCentricCubicMesh&diff=38342 Documentation/Nightly/Modules/BodyCentricCubicMesh 2014-06-20T18:38:50Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/ImageToMeshConversion|Image-To-Mesh (I2M) Conversion]]&lt;br&gt;<br /> Acknowledgments:<br /> *This work was partially supported by NIH R44 OD018334-03A, grant CCF-1139864 and by the Richard T.Cheng Endowment.<br /> <br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andrey Fedorov (CRTC), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/joomla/<br /> &lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module generates a Body Centric Cubic (BCC) mesh from a labeled image. Initially the generated mesh is homogeneous, that means does not distinguish different tissues. Later the module specifies which tissue each tetrahedron belongs to. Each tissue is capable of automatically adjusting its resolution based on its geometric complexity and the predefined subdivision criterion. The current version of the module supports a single-tissue input labeled image.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[File:brain.jpg|thumb|280px|Brain BCC mesh]]<br /> |[[File:nidus.jpg|thumb|280px|Nidus BCC mesh]]<br /> |[[File:ventricles.jpg|thumb|280px|Ventricles BCC mesh]]<br /> |}<br /> {|<br /> |[[File:brain_section.jpg|thumb|280px|Brain BCC mesh cross-section]]<br /> |[[File:nidus_section.jpg|thumb|280px|Nidus BCC mesh cross-section]]<br /> |[[File:ventricles_section.jpg|thumb|280px|Ventricles BCC mesh cross-section]]<br /> |}<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Mesh Generation Parameters:'''<br /> ** '''Size:''' Controls the size of the mesh. The smaller the value the larger the mesh. Value should be between [1,20] (default: 8).<br /> ** '''Fidelity:''' Controls the subdivision of the elements that belong to more than one image labels. The larger the value the better the conformity of the mesh on the image label boundaries. Value should be between [0.1,1] (default: 0.8).<br /> ** '''Resample Resolution:''' Controls the image resampling. Suggested value is 0 (no-resampling) for large tissues and 1 or 2 for smaller tissues. Value should be 0 or 1 or 2 (default: 0).<br /> * '''Input/Output:'''<br /> ** '''Input Labeled Image:''' The input labeled image.<br /> ** '''Output Mesh File:''' The output tetrahedral mesh in vtk file format. (default: outputMesh.vtk)<br /> |[[Image:BCCPanel.jpg|thumb|320px|User Interface]]<br /> |}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/MeshCompression]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Fedorov A., Chrisochoides N., Kikinis R., Warfield S, &quot;Tetrahedral mesh generation for medical imaging&quot;, The Insight Journal-2005 MICCAI Open-Source Workshop, 2005<br /> * Yixun Liu, Panagiotis Foteinos, Andrey Chernikov and Nikos Chrisochoides, &quot;Mesh Deformation-based Multi-tissue Mesh Generation for Brain Images&quot;, Engineering with Computers, Volume 28, pages 305-318, 2012. <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=File:BCCPanel.jpg&diff=38341 File:BCCPanel.jpg 2014-06-20T18:37:53Z <p>Fdrakopo: uploaded a new version of &quot;File:BCCPanel.jpg&quot;</p> <hr /> <div></div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38340 Documentation/Nightly/Extensions/PBNRR 2014-06-20T17:59:59Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/joomla/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Registration Parameters:'''<br /> ** '''Block Radius:''' Radius (in image voxels) of the selected image blocks in each dimension (default: 1,1,1).<br /> ** '''Window Radius:''' Radius (in image voxels) of the Block Matching window in each dimension (default: 5,5,5).<br /> ** '''Selection Fraction:''' Fraction of the selected blocks from the total number of image blocks. Value should be between [0.01,1] (default: 0.05).<br /> ** '''Rejection Fraction:''' Fraction of the rejected blocks from the number of the selected image blocks. Value should be between [0.01,1) (default: 0.25).<br /> ** '''Outlier Rejection Steps:''' Number of outlier rejection steps. Value should be between [1,20] (default: 5).<br /> ** '''Interpolation Steps:''' Number of interpolation steps. Value should be between [1,20] (default: 5).<br /> ** '''Young Modulus:''' Young Modulus of the linear bio-mechanical model (default: 0.0021 N/mm2).<br /> ** '''Poisson Ratio:''' Poisson Ratio of the linear bio-mechanical model. Value should be between [0.10,0.49] (default: 0.45).<br /> <br /> * '''Input/Output:'''<br /> ** '''Input Moving Image:''' The input moving image.<br /> ** '''Input Fixed Image:''' The input moving image.<br /> ** '''Input Mask Image:''' The input moving image.<br /> ** '''Input Mesh:''' The input moving image.<br /> ** '''Output Volume:''' Moving image to the fixed image coordinate frame (optional).<br /> ** '''Output Direct Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the moving coordinate frame to the fixed coordinate frame (optional).<br /> ** '''Output Inverse Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the fixed coordinate frame to the moving coordinate frame (optional).<br /> ** '''Output Warped Mesh:''' The warped tetrahedral mesh in vtk file format (optional).<br /> |[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Olivier Clatz, Hervé Delingette, Ion-Florin Talos, Alexandra J. Golby, Ron Kikinis, Ferenc Jolesz, Nicholas Ayache, and Simon Warfield,“Robust Non-Rigid Registration to Capture Brain Shift from Intra-Operative MRI“, IEEE Transactions on Medical Imaging, 24(11):1417-1427, Nov. 2005. <br /> * Liu Y, Kot A, Drakopoulos F, Yao C, Fedorov A, Enquobahrie A, Clatz O and Chrisochoides NP (2014), ”An ITK implementation of a physics-based non-rigid registration method for brain deformation in image-guided neurosurgery”, Frontiers in Neuroinformatics 8:33. doi: 10.3389/fninf.2014.00033<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Registration]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=File:PBNRR_panel.png&diff=38339 File:PBNRR panel.png 2014-06-20T17:59:16Z <p>Fdrakopo: uploaded a new version of &quot;File:PBNRR panel.png&quot;</p> <hr /> <div></div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38334 Documentation/Nightly/Extensions/PBNRR 2014-06-20T16:23:35Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/joomla/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Registration Parameters:'''<br /> ** '''Block Radius:''' Radius (in image voxels) of the selected image blocks in each dimension (default: 1,1,1).<br /> ** '''Window Radius:''' Radius (in image voxels) of the Block Matching window in each dimension (default: 5,5,5).<br /> ** '''Selection Fraction:''' Fraction of the selected blocks from the total number of image blocks. Value should be between [0.01,1] (default: 0.05).<br /> ** '''Rejection Fraction:''' Fraction of the rejected blocks from the number of the selected image blocks. Value should be between [0.01,1) (default: 0.25).<br /> ** '''Outlier Rejection Steps:''' Number of outlier rejection steps. Value should be between [1,20] (default: 5).<br /> ** '''Interpolation Steps:''' Number of interpolation steps. Value should be between [1,20] (default: 5).<br /> ** '''Young Modulus:''' Young Modulus of the linear bio-mechanical model (default: 0.0021 N/mm2).<br /> ** '''Poisson Ratio:''' Poisson Ratio of the linear bio-mechanical model. Value should be between [0.10,0.49] (default: 0.45).<br /> <br /> * '''Input/Output:'''<br /> ** '''Moving Image:''' The input moving image.<br /> ** '''Fixed Image:''' The input moving image.<br /> ** '''Mask Image:''' The input moving image.<br /> ** '''Mesh:''' The input moving image.<br /> ** '''Output Volume:''' Moving image to the fixed image coordinate frame (optional).<br /> ** '''Output Direct Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the moving coordinate frame to the fixed coordinate frame (optional).<br /> ** '''Output Inverse Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the fixed coordinate frame to the moving coordinate frame (optional).<br /> ** '''Output Warped Mesh:''' The warped tetrahedral mesh in vtk file format (optional).<br /> |[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Olivier Clatz, Hervé Delingette, Ion-Florin Talos, Alexandra J. Golby, Ron Kikinis, Ferenc Jolesz, Nicholas Ayache, and Simon Warfield,“Robust Non-Rigid Registration to Capture Brain Shift from Intra-Operative MRI“, IEEE Transactions on Medical Imaging, 24(11):1417-1427, Nov. 2005. <br /> * Liu Y, Kot A, Drakopoulos F, Yao C, Fedorov A, Enquobahrie A, Clatz O and Chrisochoides NP (2014), ”An ITK implementation of a physics-based non-rigid registration method for brain deformation in image-guided neurosurgery”, Frontiers in Neuroinformatics 8:33. doi: 10.3389/fninf.2014.00033<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Registration]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38333 Documentation/Nightly/Extensions/PBNRR 2014-06-20T16:22:56Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/joomla/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Registration Parameters:'''<br /> ** '''Block Radius:''' Radius (in image voxels) of the selected image blocks in each dimension (default: 1,1,1).<br /> ** '''Window Radius:''' Radius (in image voxels) of the Block Matching window in each dimension (default: 5,5,5).<br /> ** '''Selection Fraction:''' Fraction of the selected blocks from the total number of image blocks. Value should be between [0.01,1] (default: 0.05).<br /> ** '''Rejection Fraction:''' Fraction of the rejected blocks from the number of the selected image blocks. Value should be between [0.01,1) (default: 0.25).<br /> ** '''Outlier Rejection Steps:''' Number of outlier rejection steps. Value should be between [1,20] (default: 5).<br /> ** '''Interpolation Steps:''' Number of interpolation steps. Value should be between [1,20] (default: 5).<br /> ** '''Young Modulus:''' Young Modulus of the linear bio-mechanical model (default: 0.0021 N/mm2).<br /> ** '''Poisson Ratio:''' Poisson Ratio of the linear bio-mechanical model. Value should be between [0.10,0.49] (default: 0.45).<br /> <br /> * '''Input/Output:'''<br /> ** '''Moving Image:''' The input moving image.<br /> ** '''Fixed Image:''' The input moving image.<br /> ** '''Mask Image:''' The input moving image.<br /> ** '''Mesh:''' The input moving image.<br /> ** '''Output Volume:''' Moving image to the fixed image coordinate frame (optional).<br /> ** '''Output Direct Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the moving coordinate frame to the fixed coordinate frame (optional).<br /> ** '''Output Inverse Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the fixed coordinate frame to the moving coordinate frame (optional).<br /> ** '''Output Warped Mesh:''' The warped tetrahedral mesh in vtk file format (optional).<br /> |[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/BSplineDeformableRegistration]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Olivier Clatz, Hervé Delingette, Ion-Florin Talos, Alexandra J. Golby, Ron Kikinis, Ferenc Jolesz, Nicholas Ayache, and Simon Warfield,“Robust Non-Rigid Registration to Capture Brain Shift from Intra-Operative MRI“, IEEE Transactions on Medical Imaging, 24(11):1417-1427, Nov. 2005. <br /> * Liu Y, Kot A, Drakopoulos F, Yao C, Fedorov A, Enquobahrie A, Clatz O and Chrisochoides NP (2014), ”An ITK implementation of a physics-based non-rigid registration method for brain deformation in image-guided neurosurgery”, Frontiers in Neuroinformatics 8:33. doi: 10.3389/fninf.2014.00033<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Registration]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38332 Documentation/Nightly/Extensions/PBNRR 2014-06-20T16:20:48Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/joomla/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Registration Parameters:'''<br /> ** '''Block Radius:''' Radius (in image voxels) of the selected image blocks in each dimension (default: 1,1,1).<br /> ** '''Window Radius:''' Radius (in image voxels) of the Block Matching window in each dimension (default: 5,5,5).<br /> ** '''Selection Fraction:''' Fraction of the selected blocks from the total number of image blocks. Value should be between [0.01,1] (default: 0.05).<br /> ** '''Rejection Fraction:''' Fraction of the rejected blocks from the number of the selected image blocks. Value should be between [0.01,1) (default: 0.25).<br /> ** '''Outlier Rejection Steps:''' Number of outlier rejection steps. Value should be between [1,20] (default: 5).<br /> ** '''Interpolation Steps:''' Number of interpolation steps. Value should be between [1,20] (default: 5).<br /> ** '''Young Modulus:''' Young Modulus of the linear bio-mechanical model (default: 0.0021 N/mm2).<br /> ** '''Poisson Ratio:''' Poisson Ratio of the linear bio-mechanical model. Value should be between [0.10,0.49] (default: 0.45).<br /> <br /> * '''Input/Output:'''<br /> ** '''Moving Image:''' The input moving image.<br /> ** '''Fixed Image:''' The input moving image.<br /> ** '''Mask Image:''' The input moving image.<br /> ** '''Mesh:''' The input moving image.<br /> ** '''Output Volume:''' Moving image to the fixed image coordinate frame (optional).<br /> ** '''Output Direct Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the moving coordinate frame to the fixed coordinate frame (optional).<br /> ** '''Output Inverse Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the fixed coordinate frame to the moving coordinate frame (optional).<br /> ** '''Output Warped Mesh:''' The warped tetrahedral mesh in vtk file format (optional).<br /> |[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/BRAINSFit]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Olivier Clatz, Hervé Delingette, Ion-Florin Talos, Alexandra J. Golby, Ron Kikinis, Ferenc Jolesz, Nicholas Ayache, and Simon Warfield,“Robust Non-Rigid Registration to Capture Brain Shift from Intra-Operative MRI“, IEEE Transactions on Medical Imaging, 24(11):1417-1427, Nov. 2005. <br /> * Liu Y, Kot A, Drakopoulos F, Yao C, Fedorov A, Enquobahrie A, Clatz O and Chrisochoides NP (2014), ”An ITK implementation of a physics-based non-rigid registration method for brain deformation in image-guided neurosurgery”, Frontiers in Neuroinformatics 8:33. doi: 10.3389/fninf.2014.00033<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Registration]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38331 Documentation/Nightly/Extensions/PBNRR 2014-06-20T16:17:28Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/joomla/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Registration Parameters:'''<br /> ** '''Block Radius:''' Radius (in image voxels) of the selected image blocks in each dimension (default: 1,1,1).<br /> ** '''Window Radius:''' Radius (in image voxels) of the Block Matching window in each dimension (default: 5,5,5).<br /> ** '''Selection Fraction:''' Fraction of the selected blocks from the total number of image blocks. Value should be between [0.01,1] (default: 0.05).<br /> ** '''Rejection Fraction:''' Fraction of the rejected blocks from the number of the selected image blocks. Value should be between [0.01,1) (default: 0.25).<br /> ** '''Outlier Rejection Steps:''' Number of outlier rejection steps. Value should be between [1,20] (default: 5).<br /> ** '''Interpolation Steps:''' Number of interpolation steps. Value should be between [1,20] (default: 5).<br /> ** '''Young Modulus:''' Young Modulus of the linear bio-mechanical model (default: 0.0021 N/mm2).<br /> ** '''Poisson Ratio:''' Poisson Ratio of the linear bio-mechanical model. Value should be between [0.10,0.49] (default: 0.45).<br /> <br /> * '''Input/Output:'''<br /> ** '''Moving Image:''' The input moving image.<br /> ** '''Fixed Image:''' The input moving image.<br /> ** '''Mask Image:''' The input moving image.<br /> ** '''Mesh:''' The input moving image.<br /> ** '''Output Volume:''' Moving image to the fixed image coordinate frame (optional).<br /> ** '''Output Direct Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the moving coordinate frame to the fixed coordinate frame (optional).<br /> ** '''Output Inverse Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the fixed coordinate frame to the moving coordinate frame (optional).<br /> ** '''Output Warped Mesh:''' The warped tetrahedral mesh in vtk file format (optional).<br /> |[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> *[[Documentation/Nightly/Modules/BRAINSFit]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.<br /> * Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38330 Documentation/Nightly/Extensions/PBNRR 2014-06-20T16:14:54Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/joomla/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Registration Parameters:'''<br /> ** '''Block Radius:''' Radius (in image voxels) of the selected image blocks in each dimension (default: 1,1,1).<br /> ** '''Window Radius:''' Radius (in image voxels) of the Block Matching window in each dimension (default: 5,5,5).<br /> ** '''Selection Fraction:''' Fraction of the selected blocks from the total number of image blocks. Value should be between [0.01,1] (default: 0.05).<br /> ** '''Rejection Fraction:''' Fraction of the rejected blocks from the number of the selected image blocks. Value should be between [0.01,1) (default: 0.25).<br /> ** '''Outlier Rejection Steps:''' Number of outlier rejection steps. Value should be between [1,20] (default: 5).<br /> ** '''Interpolation Steps:''' Number of interpolation steps. Value should be between [1,20] (default: 5).<br /> ** '''Young Modulus:''' Young Modulus of the linear bio-mechanical model (default: 0.0021 N/mm2).<br /> ** '''Poisson Ratio:''' Poisson Ratio of the linear bio-mechanical model. Value should be between [0.10,0.49] (default: 0.45).<br /> <br /> * '''Input/Output:'''<br /> ** '''Moving Image:''' The input moving image.<br /> ** '''Fixed Image:''' The input moving image.<br /> ** '''Mask Image:''' The input moving image.<br /> ** '''Mesh:''' The input moving image.<br /> ** '''Output Volume:''' Moving image to the fixed image coordinate frame (optional).<br /> ** '''Output Direct Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the moving coordinate frame to the fixed coordinate frame (optional).<br /> ** '''Output Inverse Deformation Field:''' Transform calculated that aligns the fixed and moving image. Maps positions in the fixed coordinate frame to the moving coordinate frame (optional).<br /> ** '''Output Warped Mesh:''' The warped tetrahedral mesh in vtk file format (optional).<br /> |[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.<br /> * Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38329 Documentation/Nightly/Extensions/PBNRR 2014-06-20T16:10:47Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/joomla/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> * '''Registration Parameters:'''<br /> ** '''Block Radius:''' Radius (in image voxels) of the selected image blocks in each dimension (default: 1,1,1).<br /> ** '''Window Radius:''' Radius (in image voxels) of the Block Matching window in each dimension (default: 5,5,5).<br /> ** '''Selection Fraction:''' Fraction of the selected blocks from the total number of image blocks. Value should be between [0.01,1] (default: 0.05).<br /> ** '''Rejection Fraction:''' Fraction of the rejected blocks from the number of the selected image blocks. Value should be between [0.01,1) (default: 0.25).<br /> ** '''Outlier Rejection Steps:''' Number of outlier rejection steps. Value should be between [1,20] (default: 5).<br /> ** '''Interpolation Steps:''' Number of interpolation steps. Value should be between [1,20] (default: 5).<br /> ** '''Young Modulus:''' Young Modulus of the linear bio-mechanical model (default: 0.0021 N/mm2).<br /> ** '''Poisson Ratio:''' Poisson Ratio of the linear bio-mechanical model. Value should be between [0.10,0.49] (default: 0.45).<br /> <br /> * '''Input/Output:'''<br /> ** '''Labeled Image:''' The input labeled image.<br /> ** '''Output Mesh:''' The output tetrahedral mesh in vtk file format. (default: outputMesh.vtk)<br /> |[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.<br /> * Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=File:PBNRR_panel.png&diff=38328 File:PBNRR panel.png 2014-06-20T15:56:11Z <p>Fdrakopo: </p> <hr /> <div></div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38327 Documentation/Nightly/Extensions/PBNRR 2014-06-20T15:55:52Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/joomla/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> |[[Image:PBNRR_panel.png|thumb|280px|PBNRR UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.<br /> * Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38326 Documentation/Nightly/Extensions/PBNRR 2014-06-20T15:50:13Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/joomla/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 Input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 Output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> |[[Image:SkullStripper-3-6.png|thumb|280px|Module UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.<br /> * Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/PBNRR&diff=38325 Documentation/Nightly/Extensions/PBNRR 2014-06-20T15:49:39Z <p>Fdrakopo: </p> <hr /> <div>&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt;<br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br /> {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> Extension: [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]]&lt;br&gt;<br /> Acknowledgments:<br /> This work is funded mainly by the ARRA funds for the ITK-v4 implementation with grant number:NLMA2D2201000586P. In addition, this work is supported in part by NSFgrants:CCF-1139864, CCF-1136538, and CSI-1136536 and by the John Simon Guggenheim Foundation and the Richard T.Cheng Endowment.&lt;br&gt;<br /> Author: Fotis Drakopoulos&lt;br&gt;<br /> Contributors: Fotis Drakopoulos (CRTC), Yixun Liu (CRTC), Andriy Kot (CRTC), Andrey Fedorov (SPL B&amp;W Harvard), Olivier Clatz (Asclepios INRIA), Nikos Chrisochoides (CRTC)&lt;br&gt;<br /> Contact: Nikos Chrisochoides, &lt;email&gt;npchris@gmail.com&lt;/email&gt;&lt;br&gt;<br /> Website: https://crtc.cs.odu.edu/joomla/&lt;br&gt;<br /> License: BSD&lt;br&gt;<br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> {{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |Image:CRTC_logo.jpg|Center for Real-time Computing <br /> }}<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> The module Non-Rigid Registers a moving to a fixed MRI. It uses a linear homogeneous bio-mechanical model to compute a dense deformation field that defines a transformation for every point in the fixed image to the moving image. The method includes three components (Feature Point Selection, Block Matching and Finite Element Solver) combine together to provide a user-friendly interface.<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> {|<br /> |[[Image:case1_input.png|thumb|450px| '''Case1 input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case1_output.png|thumb|450px| '''Case1 output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> {|<br /> |[[Image:case2_input.png|thumb|450px| '''Case2 input'''; top left: moving image, top right: mesh, bottom left: fixed image, bottom right: mask image.]]<br /> |[[Image:case2_output.png|thumb|450px| '''Case2 output'''; top left: warped image, top right: warped mesh, bottom left: direct deformation field, bottom right: inverse deformation field.]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> <br /> {|<br /> |<br /> |[[Image:SkullStripper-3-6.png|thumb|280px|Module UI]]<br /> |}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> * Xiaodong Tao, Ming-ching Chang, “A Skull Stripping Method Using Deformable Surface and Tissue Classification”, SPIE Medical Imaging, San Diego, CA, 2010.<br /> * Ming-ching Chang, Xiaodong Tao “Subvoxel Segmentation and Representation of Brain Cortex Using Fuzzy Clustering and Gradient Vector Diffusion”, SPIE Medical Imaging, San Diego, CA, 2010.<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> [[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]<br /> &lt;!-- ---------------------------- --&gt;</div> Fdrakopo