https://www.slicer.org/w/api.php?action=feedcontributions&feedformat=atom&user=Ikolesov 2026-04-09T00:36:03Z User contributions MediaWiki 1.33.0 https://www.slicer.org/w/index.php?title=Developer_Meetings/20141021&diff=39324 2014-10-21T16:20:01Z

<p>Ikolesov: </p> <hr /> <div>== To discuss ==<br /> <br /> * Fiber bundle issues: What is the status regarding these issues?<br /> ** Fiber bundle issues:<br /> *** [http://na-mic.org/Mantis/view.php?id=3863 3863: slicer crashes when I display tract tubes on a slice ] <br /> *** [http://na-mic.org/Mantis/view.php?id=3462 3462: ModelMaker functionality breaks display of Slice views ]<br /> *** [http://na-mic.org/Mantis/view.php?id=3678 3678: fiber bundle hierarchies are broken]<br /> ** CarreraSlice/FastGrowCut issues:<br /> *** Slicer build errors on Mac OS<br /> *** http://slicer.cdash.org/viewBuildError.php?buildid=284706</div>

Ikolesov https://www.slicer.org/w/index.php?title=Developer_Meetings/20141021&diff=39323 2014-10-21T16:18:13Z

<p>Ikolesov: </p> <hr /> <div>== To discuss ==<br /> <br /> * Fiber bundle issues: What is the status regarding these issues?<br /> ** Fiber bundle issues:<br /> *** [http://na-mic.org/Mantis/view.php?id=3863 3863: slicer crashes when I display tract tubes on a slice ] <br /> *** [http://na-mic.org/Mantis/view.php?id=3462 3462: ModelMaker functionality breaks display of Slice views ]<br /> *** [http://na-mic.org/Mantis/view.php?id=3678 3678: fiber bundle hierarchies are broken]<br /> *** Slicer build errors on Mac OS and CarreraSlice/FastGrowCut</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules&diff=37583 2014-04-11T17:36:41Z

<p>Ikolesov: /* Segmentation */</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 /> <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 /> <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/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>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/CarreraSliceInteractiveSegmenter&diff=37582 2014-04-11T17:22:26Z

<p>Ikolesov: Created page with '&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt; &lt;!-- ---------------------------- --&gt; {{documentation/{{documentation/version}}/module-header}} &lt;!-- -----------------------…'</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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Stony Brook University&lt;br&gt;<br /> Author: Liangjia Zhu, Stony Brook University&lt;br&gt;<br /> Author: Yi Gao, University of Alabama Birmingham&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, Stony Brook University&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the CarreraSlice interactive segmentation method. The computation is initialized using an improved GrowCut implementation and refined by an interactive, level set based segmentation algorithm, KSlice. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “CarreraSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:CarreraSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( CarreraSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> Step 6.) Initialize the segmentation using fast GrowCut<br /> * (a) go to PaintEffect to draw seed regions (label 1 for foreground and 2 for background), then press 'G' to run fast GrowCut.<br /> [[File:FGCSeed.png|500px]] [[File:FGCSeg1.png|500px]]<br /> <br /> * (b) If not satified, press 'S' to toggle between seed image and segmentation result. Edit on the seed image to reduce over/under segmentaions. <br /> [[File:FGCSeed2.png|500px]]<br /> <br /> * (c) Once finished editing on the seed image, press 'G' to run fast GrowCut again. <br /> [[File:FGCSeg2.png|500px]]<br /> <br /> The steps 6 (b) and (c) may be repeated a couple of times until satisfied.<br /> <br /> Step 7.) Once satisfied with the initialization, press 'M' to start KSlice interactive segmentation. The energy functionals available are:<br /> * (a) press 'F' for local-global Chan-Vese segmentation<br /> * (b) press 'U' for mean curvature smoothing<br /> * (c) press 'E' for Chan-Vese segmentation<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> *(Used in any order) A segmenting surface may leak into undesirable areas, based purely on image data. It is the user's job to guide the evolution process. A user can provide positive input (drawing) by selecting a paint tool, painting in areas which should be part of the object of interest but are not. Or, the user can provide negative input (erasing) by pressing &quot;A&quot; (toggle label value between 0 and the originally selected label). An example of a user correction is going from <br /> <br /> [[File:KSliceNegativeInput.png|500px]]<br /> <br /> to<br /> <br /> [[File:KSliceCorrectedUI.png|500px]]<br /> <br /> * (Used in any order) Certain image regions (depending on the energy chosen and the image itself) may be highly attractive for the evolving contour despite being incorrect according to the user's expert knowledge. He has two options. First, apply repeated input several times (soft user constraints). Second, he can press &quot;B&quot; (toggle between soft/hard constraints) to increase the weight on his inputs, essentially making them hard constraints. Further, constraints can be provided pre-emptively, by erasing/drawing in regions before a contour has reached these areas to prevent leaks in the future or expedite the evolution process, respectively. <br /> <br /> <br /> *(Used in any order) Press &quot;F&quot; to run the contour in 3D, similarly to Step.7 but using an alternative energy, the Local Global Chan-Vese. The user can switch the energy he is using at any time.<br /> <br /> * (Used in any order) Press &quot;U&quot; to run the contour in 3D, similarly to Step.7 but using an alternative energy, the curvature flow. The user can switch the energy he is using at any time.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> * (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOnMeningioma.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> * Examine the current segmentation by flipping through the 2D viewers, providing input to guide the evolution. <br /> <br /> [[File:ExampleUIDuringProcess.png|500px]] <br /> <br /> <br /> <br /> * Repeat previous steps (or any subset of them) until convergence to the desired segmentation.<br /> <br /> [[File:KSliceFinalSegMeningioma.png|500px]] <br /> <br /> <br /> *Once satisfied with the segmentation, stop CarreraSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopInteractiveSegmenter.png|500px]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There are two parameters to set: the radius that sets the band around the current initialisation in which image data is considered (for Local-Global Chan-Vese energy) and the number of contour iterations. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user). The number of iterations refers to the time for which the segmenting surface is allowed to evolve before querying the user for input. A small number allows the user to catch the surface before a large error is made, reducing corrective inputs required but may be tedious/slow.<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions&diff=37581 2014-04-11T17:19:40Z

<p>Ikolesov: /* 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/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 /> ** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy]]<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/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]] (Andinet Enquobahrie, Luis G. Torres)<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 /> <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>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter&diff=37166 2014-01-30T23:46:18Z

<p>Ikolesov: </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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Stony Brook University&lt;br&gt;<br /> Author: Liangjia Zhu, Stony Brook University&lt;br&gt;<br /> Author: Yi Gao, University of Alabama Birmingham&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, Stony Brook University&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the CarreraSlice interactive segmentation method. The computation is initialized using an improved GrowCut implementation and refined by an interactive, level set based segmentation algorithm, KSlice. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “CarreraSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:CarreraSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( CarreraSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> Step 6.) Initialize the segmentation using fast GrowCut<br /> * (a) go to PaintEffect to draw seed regions (label 1 for foreground and 2 for background), then press 'G' to run fast GrowCut.<br /> [[File:FGCSeed.png|500px]] [[File:FGCSeg1.png|500px]]<br /> <br /> * (b) If not satified, press 'S' to toggle between seed image and segmentation result. Edit on the seed image to reduce over/under segmentaions. <br /> [[File:FGCSeed2.png|500px]]<br /> <br /> * (c) Once finished editing on the seed image, press 'G' to run fast GrowCut again. <br /> [[File:FGCSeg2.png|500px]]<br /> <br /> The steps 6 (b) and (c) may be repeated a couple of times until satisfied.<br /> <br /> Step 7.) Once satisfied with the initialization, press 'M' to start KSlice interactive segmentation. The energy functionals available are:<br /> * (a) press 'F' for local-global Chan-Vese segmentation<br /> * (b) press 'U' for mean curvature smoothing<br /> * (c) press 'E' for Chan-Vese segmentation<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> *(Used in any order) A segmenting surface may leak into undesirable areas, based purely on image data. It is the user's job to guide the evolution process. A user can provide positive input (drawing) by selecting a paint tool, painting in areas which should be part of the object of interest but are not. Or, the user can provide negative input (erasing) by pressing &quot;A&quot; (toggle label value between 0 and the originally selected label). An example of a user correction is going from <br /> <br /> [[File:KSliceNegativeInput.png|500px]]<br /> <br /> to<br /> <br /> [[File:KSliceCorrectedUI.png|500px]]<br /> <br /> * (Used in any order) Certain image regions (depending on the energy chosen and the image itself) may be highly attractive for the evolving contour despite being incorrect according to the user's expert knowledge. He has two options. First, apply repeated input several times (soft user constraints). Second, he can press &quot;B&quot; (toggle between soft/hard constraints) to increase the weight on his inputs, essentially making them hard constraints. Further, constraints can be provided pre-emptively, by erasing/drawing in regions before a contour has reached these areas to prevent leaks in the future or expedite the evolution process, respectively. <br /> <br /> <br /> *(Used in any order) Press &quot;F&quot; to run the contour in 3D, similarly to Step.7 but using an alternative energy, the Local Global Chan-Vese. The user can switch the energy he is using at any time.<br /> <br /> * (Used in any order) Press &quot;U&quot; to run the contour in 3D, similarly to Step.7 but using an alternative energy, the curvature flow. The user can switch the energy he is using at any time.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> * (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOnMeningioma.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> * Examine the current segmentation by flipping through the 2D viewers, providing input to guide the evolution. <br /> <br /> [[File:ExampleUIDuringProcess.png|500px]] <br /> <br /> <br /> <br /> * Repeat previous steps (or any subset of them) until convergence to the desired segmentation.<br /> <br /> [[File:KSliceFinalSegMeningioma.png|500px]] <br /> <br /> <br /> *Once satisfied with the segmentation, stop CarreraSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopInteractiveSegmenter.png|500px]]<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There are two parameters to set: the radius that sets the band around the current initialisation in which image data is considered (for Local-Global Chan-Vese energy) and the number of contour iterations. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user). The number of iterations refers to the time for which the segmenting surface is allowed to evolve before querying the user for input. A small number allows the user to catch the surface before a large error is made, reducing corrective inputs required but may be tedious/slow.<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Slicer4:VisualBlog&diff=37016 2014-01-15T23:37:22Z

<p>Ikolesov: </p> <hr /> <div>This is the Slicer 4 visual blog. Please click [[Slicer3:VisualBlog| here]] if you are looking for the old Slicer 3 visual blog.<br /> <br /> &lt;gallery caption=&quot;2013&quot; widths=&quot;200px&quot; perrow=&quot;4&quot;&gt;<br /> Image:SlicerIGT-VisualBlog2013.png| Some applications of the SlicerIGT extension for image-guided and navigated medical interventions. For more information see the [http://www.slicerigt.org Slicer IGT website].<br /> Image:UKFTractography_CC.jpg|[http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/UKFTractography UKFTractography] is a module for computing tractography of DWI images using an unscented Kalman filter. Because of its 2-tensor algorithm, it is able to model fiber crossings and capture many more fibers than a single tensor algorithm.<br /> Image:SPV1.png|[http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/ShapePopulationViewer ShapePopulationViewer] is an external tool that allows the user to dynamically interact with multiple surfaces at the same time : an interesting tool for shape visualisation and comparison. It now is available as a Slicer Extension.<br /> Image:SlicerRT_0.13_SubjectHierarchy_ProstateEclipseLoaded.png|[http://www.na-mic.org/Wiki/index.php/2014_Winter_Project_Week:SubjectHierarchy The Subject hierarchy module and mechanism] organizes and handles loaded data in the RT extension package, providing processing and analysis features through plugins. It aspires to be a convenient central organizing point for many of the operations that 3D Slicer and its extensions perform.<br /> Image:DownloadFile 2.jpg|[[Documentation/4.3/Modules/DataStore|The Data Store]] allows a user to easily upload and download MRB files. <br /> Image:SlicerRT ContourRepresentations.png|[[Documentation/4.3/Modules/Contours|The Contours module]] manages contours in the RT extension package.<br /> Image:MultiVolume-4.3.0-update.png| [[Documentation/4.3/Modules/MultiVolumeExplorer|MultiVolumeExplorer module]] has been updated to include the capability to plot multivolume pixel values from 2 multivolumes at the same time. This feature is particularly helpful while visualizing the results of model fits, such as those produced by the updated [[Documentation/4.3/Modules/PkModeling|PkModeling extension]].<br /> Image:MatlabBridgeLogo.png| A new extension allows to run matlab scripts without having to recompile Slicer. For more information see [[Documentation/Nightly/Extensions/MatlabBridge|'''here''']]<br /> Image:ExtensionManagerScreen Shot 2013-05-23 at 9.40.23 PM.png| Extension Manager, the slicer multiplatform Appstore is open for business and free.<br /> Image:ScreenshotLobeSegmentation.png| Semi-automatic lobe segmentation for regional lung disease analysis as part of the Chest Imaging Platform funded by NHLBI 1R01HL116931<br /> Image:CMRToolkit.png|The [http://capulet.med.utah.edu/namic/cmrslicer Cardiac MR Extension] provides tools for segmentation and analysis of heart tissue and structure for treatment and diagnosis of Atrial Fibrillation.<br /> Image:CarreraSliceBlogEntry.png| [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] is an interactive segmentation tool. It combines a fast implementation of the GrowCut algorithm for the 'initialization' phase with KSlice, an interactive algorithm based on Level Sets, for the 'refinement' stage.<br /> &lt;/gallery&gt;<br /> &lt;gallery caption=&quot;2012&quot; widths=&quot;200px&quot; perrow=&quot;4&quot;&gt;<br /> Image:BoxChart.png| A box plot<br /> Image:2012-09-07-FetalBrain.png| Fetal brain development. The visualization is using volume rendering and the Multivolume modules in Slicer 4. Click [[media:FetalBrainGowth.mov|'''here''']] for the full movie (~24mb). Data downloaded from [http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Fetal Imperial College].<br /> Image:Screen Shot 2012-09-05 at 10.01.35 AM.png|Leveraging multi viewer layout to arrange 6 slices in the 3D viewer<br /> Image:ComplexQueryWithImage.jpg|Visualization of complex query &quot;motor system + mass + straight gyrus&quot; using the faceted query module<br /> Image:Screen Shot 2012-05-30 at 8.03.23 AM.png| Fibers colored by their mean orientation is now available in the Tractography Display module<br /> Image:SlicerRT-0.2_screenshot.png|[https://www.assembla.com/spaces/slicerrt/milestones/1089853-slicerrt-0-2-release SlicerRT 0.2] has been released! [https://www.assembla.com/spaces/slicerrt/ SlicerRT] is 3D Slicer with extensions for radiotherapy research, which is developed by SparKit project with the contributions from Slicer community.<br /> Image:Screen Shot 2012-04-11 at 8.07.36 AM.png|The new extension manager<br /> Image:Screen Shot 2012-04-11 at 8.11.59 AM.png|Up to date download statistics<br /> Image:Screen Shot 2012-04-05 at 11.35.08 AM.png|A combination of ROI cropping of streamlines, fiducial based seeding and labelmap seeding allows to assess the deformation of streamlines which are due to tumor based deformations.<br /> Image:2012-03-05-downloadpage.png|New download page which highlights the operating system of the downloading system.<br /> Image:2012-03-04-Welcome.png|New look for the Welcome module and the &quot;Load/Save&quot; toolbar<br /> Image:2012-03-04-DWI2FBT.png|Step one of the DWI to Full-brain tractography wizard<br /> Image:2012-03-04-SliceViewerControllers.png|Improved 2-stage user interface for the Slice Viewer Controllers<br /> Image:2012-03-04-DicomWidget.png|Updated Dicom Module<br /> Image:2012-03-04-CoreModuleIcons.png|Updated Icons for the Core Modules<br /> Image:2012-03-04-CompareViews.png|Updated CompareViewers and Viewer Controler Module<br /> Image:Screen Shot 2012-02-23 at 7.53.51 AM.png|MultiVolumeExplorer with support for charting. See [[Documentation/Snapshot/Modules/MultiVolumeExplorer|here]] for more information.<br /> Image:Screen Shot 2012-02-09 at 10.11.08 AM.png|[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] with charting and visualization<br /> Image:3D Slicer 4.0.1.2012-02-03 180.png|Image Quantification with Label Statistics, Charting, and Volume Rendering<br /> Image:Slicer2011-gource.png|Frame from a movie of slicer code activity in 2011. See '''[http://boggs.bwh.harvard.edu/slicer/slicer4-2011-gource.x264.mp4 the full movie here]'''. Made with [http://code.google.com/p/gource/ gource]. Inspired by a [http://vimeo.com/33989053 an ITKv4 gource movie]<br /> Image:AnEarlyChartView.png|A ChartView using QWebView and jqPlot with plots defined in MRML<br /> Image:ALaterChartView.png|A ChartView using QWebView and jqPlot with plots defined in MRML<br /> Image:ABarChartView.png|A bar chart tie MRML to a QWebView<br /> &lt;/gallery&gt;<br /> &lt;gallery caption=&quot;2011&quot; widths=&quot;200px&quot; perrow=&quot;4&quot;&gt;<br /> Image:Prostate multiparametric visualization Slicer4.png|Compareviewers<br /> Image:Slicer4_ChangeTracker_Ad.png|ChangeTracker visualization of analysis results<br /> Image:Slicer4-SceneViewGUI.jpeg|Sceneview Module<br /> Image:Selection 142.png|Dicom widget<br /> Image:3D Slicer 4.0.gamma-2011-10-20 141.png|Endoscopy module<br /> Image:VolumeRendering-CTA-2011.png|Volumerendering of a CT angiogram<br /> Image:Tumor-Volume-Rendering-PostGad-2011.png|Volumerendering of a subvolume of a post Gadolinium T1 weighted image of a GBM. Note the relation of surrounding vessels to the tumor.<br /> Image:2011-11-12-CroppingWholeBrainTractography-detail.png|Note the deformation of the corpus callosum fibers<br /> Image:2011-11-12-CroppingWholeBrainTractography.png|Using an ROI to crop streamlines from a whole brain tractography. The streamlines display color by orientation, the ellipsoids are displaying fractional anisotropy.<br /> Image:Screen Shot 2011-11-02 at 1.52.42 PM.png|Annotation module 2011-11<br /> Image:MainGUI-2011-11.png|Main Gui with pop-up slice controllers<br /> Image:DataProbe-2011-11.png|The Data Probe<br /> Image:ModelsModule-2011-11.png|Models organized in a hierarchy<br /> Image:Conventional-Widescreen-10-2011.png|New Look Oct 2011<br /> Image:QSlicerVolumeRenderingModule-DualView.png|Dual camera, dual 3D viewer<br /> Image:4.0-Main-GUI-Facelift.png|After the facelift for the GUI<br /> Image:QSlicerModelsModule.png|New models module appearance<br /> Image:SlicerWithVolumeRendering.png|Slicer4 with Volume Rendering<br /> Image:Slicer4-AnnotationGUI.jpg|Slicer4 Annotation Module<br /> Image:SlicerWithDTI.png|Glyph display on cross-sections<br /> Image:FirstCompareViewInSlicer4-2011.png| First CompareView in Slicer4 2011<br /> Image:2011-01-24-Annotation.png| Slicer 4 Annotation Module 2011-01-24<br /> Image:2011-01-24-Annotation.png| Slicer 4 Annotation Module 2011-01-24<br /> Image:LiveUltrasoundModule-Slicer4.jpg| Slicer 4 Live ultrasound module for IGT spine procedures<br /> Image:LiveUltrasoundModule-Slicer4_2.jpg| Slicer 4 Live ultrasound module for IGT prostate procedures<br /> &lt;/gallery&gt;<br /> <br /> &lt;gallery caption=&quot;2010&quot; widths=&quot;200px&quot; perrow=&quot;4&quot;&gt;<br /> Image:2010-SlicerAM QtAnnotation.png| Slicer 4 Annotation Module<br /> Image:SlicerQT-2009-12-10.png|Slicer with Qt only<br /> Image:QSlicerROIModule.png| ROI Module<br /> &lt;/gallery&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Slicer4:VisualBlog&diff=37015 2014-01-15T23:36:42Z

<p>Ikolesov: </p> <hr /> <div>This is the Slicer 4 visual blog. Please click [[Slicer3:VisualBlog| here]] if you are looking for the old Slicer 3 visual blog.<br /> <br /> &lt;gallery caption=&quot;2013&quot; widths=&quot;200px&quot; perrow=&quot;4&quot;&gt;<br /> Image:SlicerIGT-VisualBlog2013.png| Some applications of the SlicerIGT extension for image-guided and navigated medical interventions. For more information see the [http://www.slicerigt.org Slicer IGT website].<br /> Image:UKFTractography_CC.jpg|[http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/UKFTractography UKFTractography] is a module for computing tractography of DWI images using an unscented Kalman filter. Because of its 2-tensor algorithm, it is able to model fiber crossings and capture many more fibers than a single tensor algorithm.<br /> Image:SPV1.png|[http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/ShapePopulationViewer ShapePopulationViewer] is an external tool that allows the user to dynamically interact with multiple surfaces at the same time : an interesting tool for shape visualisation and comparison. It now is available as a Slicer Extension.<br /> Image:SlicerRT_0.13_SubjectHierarchy_ProstateEclipseLoaded.png|[http://www.na-mic.org/Wiki/index.php/2014_Winter_Project_Week:SubjectHierarchy The Subject hierarchy module and mechanism] organizes and handles loaded data in the RT extension package, providing processing and analysis features through plugins. It aspires to be a convenient central organizing point for many of the operations that 3D Slicer and its extensions perform.<br /> Image:DownloadFile 2.jpg|[[Documentation/4.3/Modules/DataStore|The Data Store]] allows a user to easily upload and download MRB files. <br /> Image:SlicerRT ContourRepresentations.png|[[Documentation/4.3/Modules/Contours|The Contours module]] manages contours in the RT extension package.<br /> Image:MultiVolume-4.3.0-update.png| [[Documentation/4.3/Modules/MultiVolumeExplorer|MultiVolumeExplorer module]] has been updated to include the capability to plot multivolume pixel values from 2 multivolumes at the same time. This feature is particularly helpful while visualizing the results of model fits, such as those produced by the updated [[Documentation/4.3/Modules/PkModeling|PkModeling extension]].<br /> Image:MatlabBridgeLogo.png| A new extension allows to run matlab scripts without having to recompile Slicer. For more information see [[Documentation/Nightly/Extensions/MatlabBridge|'''here''']]<br /> Image:ExtensionManagerScreen Shot 2013-05-23 at 9.40.23 PM.png| Extension Manager, the slicer multiplatform Appstore is open for business and free.<br /> Image:ScreenshotLobeSegmentation.png| Semi-automatic lobe segmentation for regional lung disease analysis as part of the Chest Imaging Platform funded by NHLBI 1R01HL116931<br /> Image:CMRToolkit.png|The [http://capulet.med.utah.edu/namic/cmrslicer Cardiac MR Extension] provides tools for segmentation and analysis of heart tissue and structure for treatment and diagnosis of Atrial Fibrillation.<br /> Image:CarreraSliceBlogEntry.png| [https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter CarreraSlice] is an interactive segmentation tool. It combines a fast implementation of the GrowCut algorithm for the 'initialization' phase with KSlice, an interactive algorithm based on Level Sets, for the 'refinement' stage. Starting from user seeds defining the background and target, a segmentation of manual quality can be achieved quickly..<br /> &lt;/gallery&gt;<br /> &lt;gallery caption=&quot;2012&quot; widths=&quot;200px&quot; perrow=&quot;4&quot;&gt;<br /> Image:BoxChart.png| A box plot<br /> Image:2012-09-07-FetalBrain.png| Fetal brain development. The visualization is using volume rendering and the Multivolume modules in Slicer 4. Click [[media:FetalBrainGowth.mov|'''here''']] for the full movie (~24mb). Data downloaded from [http://biomedic.doc.ic.ac.uk/brain-development/index.php?n=Main.Fetal Imperial College].<br /> Image:Screen Shot 2012-09-05 at 10.01.35 AM.png|Leveraging multi viewer layout to arrange 6 slices in the 3D viewer<br /> Image:ComplexQueryWithImage.jpg|Visualization of complex query &quot;motor system + mass + straight gyrus&quot; using the faceted query module<br /> Image:Screen Shot 2012-05-30 at 8.03.23 AM.png| Fibers colored by their mean orientation is now available in the Tractography Display module<br /> Image:SlicerRT-0.2_screenshot.png|[https://www.assembla.com/spaces/slicerrt/milestones/1089853-slicerrt-0-2-release SlicerRT 0.2] has been released! [https://www.assembla.com/spaces/slicerrt/ SlicerRT] is 3D Slicer with extensions for radiotherapy research, which is developed by SparKit project with the contributions from Slicer community.<br /> Image:Screen Shot 2012-04-11 at 8.07.36 AM.png|The new extension manager<br /> Image:Screen Shot 2012-04-11 at 8.11.59 AM.png|Up to date download statistics<br /> Image:Screen Shot 2012-04-05 at 11.35.08 AM.png|A combination of ROI cropping of streamlines, fiducial based seeding and labelmap seeding allows to assess the deformation of streamlines which are due to tumor based deformations.<br /> Image:2012-03-05-downloadpage.png|New download page which highlights the operating system of the downloading system.<br /> Image:2012-03-04-Welcome.png|New look for the Welcome module and the &quot;Load/Save&quot; toolbar<br /> Image:2012-03-04-DWI2FBT.png|Step one of the DWI to Full-brain tractography wizard<br /> Image:2012-03-04-SliceViewerControllers.png|Improved 2-stage user interface for the Slice Viewer Controllers<br /> Image:2012-03-04-DicomWidget.png|Updated Dicom Module<br /> Image:2012-03-04-CoreModuleIcons.png|Updated Icons for the Core Modules<br /> Image:2012-03-04-CompareViews.png|Updated CompareViewers and Viewer Controler Module<br /> Image:Screen Shot 2012-02-23 at 7.53.51 AM.png|MultiVolumeExplorer with support for charting. See [[Documentation/Snapshot/Modules/MultiVolumeExplorer|here]] for more information.<br /> Image:Screen Shot 2012-02-09 at 10.11.08 AM.png|[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] with charting and visualization<br /> Image:3D Slicer 4.0.1.2012-02-03 180.png|Image Quantification with Label Statistics, Charting, and Volume Rendering<br /> Image:Slicer2011-gource.png|Frame from a movie of slicer code activity in 2011. See '''[http://boggs.bwh.harvard.edu/slicer/slicer4-2011-gource.x264.mp4 the full movie here]'''. Made with [http://code.google.com/p/gource/ gource]. Inspired by a [http://vimeo.com/33989053 an ITKv4 gource movie]<br /> Image:AnEarlyChartView.png|A ChartView using QWebView and jqPlot with plots defined in MRML<br /> Image:ALaterChartView.png|A ChartView using QWebView and jqPlot with plots defined in MRML<br /> Image:ABarChartView.png|A bar chart tie MRML to a QWebView<br /> &lt;/gallery&gt;<br /> &lt;gallery caption=&quot;2011&quot; widths=&quot;200px&quot; perrow=&quot;4&quot;&gt;<br /> Image:Prostate multiparametric visualization Slicer4.png|Compareviewers<br /> Image:Slicer4_ChangeTracker_Ad.png|ChangeTracker visualization of analysis results<br /> Image:Slicer4-SceneViewGUI.jpeg|Sceneview Module<br /> Image:Selection 142.png|Dicom widget<br /> Image:3D Slicer 4.0.gamma-2011-10-20 141.png|Endoscopy module<br /> Image:VolumeRendering-CTA-2011.png|Volumerendering of a CT angiogram<br /> Image:Tumor-Volume-Rendering-PostGad-2011.png|Volumerendering of a subvolume of a post Gadolinium T1 weighted image of a GBM. Note the relation of surrounding vessels to the tumor.<br /> Image:2011-11-12-CroppingWholeBrainTractography-detail.png|Note the deformation of the corpus callosum fibers<br /> Image:2011-11-12-CroppingWholeBrainTractography.png|Using an ROI to crop streamlines from a whole brain tractography. The streamlines display color by orientation, the ellipsoids are displaying fractional anisotropy.<br /> Image:Screen Shot 2011-11-02 at 1.52.42 PM.png|Annotation module 2011-11<br /> Image:MainGUI-2011-11.png|Main Gui with pop-up slice controllers<br /> Image:DataProbe-2011-11.png|The Data Probe<br /> Image:ModelsModule-2011-11.png|Models organized in a hierarchy<br /> Image:Conventional-Widescreen-10-2011.png|New Look Oct 2011<br /> Image:QSlicerVolumeRenderingModule-DualView.png|Dual camera, dual 3D viewer<br /> Image:4.0-Main-GUI-Facelift.png|After the facelift for the GUI<br /> Image:QSlicerModelsModule.png|New models module appearance<br /> Image:SlicerWithVolumeRendering.png|Slicer4 with Volume Rendering<br /> Image:Slicer4-AnnotationGUI.jpg|Slicer4 Annotation Module<br /> Image:SlicerWithDTI.png|Glyph display on cross-sections<br /> Image:FirstCompareViewInSlicer4-2011.png| First CompareView in Slicer4 2011<br /> Image:2011-01-24-Annotation.png| Slicer 4 Annotation Module 2011-01-24<br /> Image:2011-01-24-Annotation.png| Slicer 4 Annotation Module 2011-01-24<br /> Image:LiveUltrasoundModule-Slicer4.jpg| Slicer 4 Live ultrasound module for IGT spine procedures<br /> Image:LiveUltrasoundModule-Slicer4_2.jpg| Slicer 4 Live ultrasound module for IGT prostate procedures<br /> &lt;/gallery&gt;<br /> <br /> &lt;gallery caption=&quot;2010&quot; widths=&quot;200px&quot; perrow=&quot;4&quot;&gt;<br /> Image:2010-SlicerAM QtAnnotation.png| Slicer 4 Annotation Module<br /> Image:SlicerQT-2009-12-10.png|Slicer with Qt only<br /> Image:QSlicerROIModule.png| ROI Module<br /> &lt;/gallery&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=File:CarreraSliceBlogEntry.png&diff=37014 2014-01-15T23:29:04Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:CarreraSliceEffect.png&diff=36894 2013-12-26T19:02:25Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter&diff=36893 2013-12-26T19:01:46Z

<p>Ikolesov: </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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Stony Brook University&lt;br&gt;<br /> Author: LiangJia Zhu, Stony Brook University&lt;br&gt;<br /> Author: Yi Gao, University of Alabama Birmingham&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, Stony Brook University&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the CarreraSlice interactive segmentation method. The computation is initialized using an improved GrowCut implementation and refined by an interactive, level set based segmentation algorithm, KSlice. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “CarreraSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:CarreraSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( CarreraSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> Step 6.) Initialize the segmentation using 2 labels (foreground and background), then press 'G' to run fast GrowCut.<br /> <br /> Step 7.) Once satisfied with the initialization, press 'M' to work with KSlice.<br /> <br /> Step 8.) Select the rectangle tool(or any other painting tool).<br /> <br /> [[File:ImplicitRectangle.png|50px]]<br /> <br /> and initialize CarreraSlice in a 2D slice by drawing inside the structure of interest.<br /> <br /> [[File:KSliceInitMeningioma.png|500px]]<br /> <br /> <br /> Step 9.) Press the “C” key to copy the current initialization in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice. Once this procedure has been repeated several times, we have initialized the surface to a cube in 3D.<br /> <br /> [[File:KSliceInit3DCube.png|500px]]<br /> <br /> <br /> Step 10.) To evolve the 2D contour on a slice, hover the mouse over a 2D view plane, press “Q”.<br /> <br /> [[File:KSlice2DEvolve.png|500px]]<br /> <br /> <br /> <br /> Step 11.) Evolve the contour in 3D by pressing &quot;E&quot; to use the Chan-Vese energy.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 12.)(Used in any order) A segmenting surface may leak into undesirable areas, based purely on image data. It is the user's job to guide the evolution process. A user can provide positive input (drawing) by selecting a paint tool, painting in areas which should be part of the object of interest but are not. Or, the user can provide negative input (erasing) by pressing &quot;A&quot; (toggle label value between 0 and the originally selected label). An example of a user correction is going from <br /> <br /> [[File:KSliceNegativeInput.png|500px]]<br /> <br /> to<br /> <br /> [[File:KSliceCorrectedUI.png|500px]]<br /> <br /> Step 13.) (Used in any order) Certain image regions (depending on the energy chosen and the image itself) may be highly attractive for the evolving contour despite being incorrect according to the user's expert knowledge. He has two options. First, apply repeated input several times (soft user constraints). Second, he can press &quot;B&quot; (toggle between soft/hard constraints) to increase the weight on his inputs, essentially making them hard constraints. Further, constraints can be provided pre-emptively, by erasing/drawing in regions before a contour has reached these areas to prevent leaks in the future or expedite the evolution process, respectively. <br /> <br /> <br /> Step 14.)(Used in any order) Press &quot;F&quot; to run the contour in 3D, similarly to Step.11 but using an alternative energy, the Local Global Chan-Vese. The user can switch the energy he is using at any time.<br /> <br /> Step 15.) (Used in any order) Press &quot;U&quot; to run the contour in 3D, similarly to Step.11 but using an alternative energy, the curvature flow. The user can switch the energy he is using at any time.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 16.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOnMeningioma.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 17.) Examine the current segmentation by flipping through the 2D viewers, providing input as in Step.12 to guide the evolution. <br /> <br /> [[File:ExampleUIDuringProcess.png|500px]] <br /> <br /> <br /> <br /> Step 18.) Repeat steps 10-15 (or any subset of them) until convergence to the desired segmentation.<br /> <br /> [[File:KSliceFinalSegMeningioma.png|500px]] <br /> <br /> <br /> Step 19.) Once satisfied with the segmentation, stop CarreraSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopInteractiveSegmenter.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There are two parameters to set: the radius that sets the band around the current initialisation in which image data is considered (for Local-Global Chan-Vese energy) and the number of contour iterations. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user). The number of iterations refers to the time for which the segmenting surface is allowed to evolve before querying the user for input. A small number allows the user to catch the surface before a large error is made, reducing corrective inputs required but may be tedious/slow.<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/CarreraSliceInteractiveSegmenter&diff=36892 2013-12-26T18:56:13Z

<p>Ikolesov: Created page with '&lt;noinclude&gt;{{documentation/versioncheck}}&lt;/noinclude&gt; &lt;!-- ---------------------------- --&gt; {{documentation/{{documentation/version}}/module-header}} &lt;!-- -----------------------…'</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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Stony Brook University&lt;br&gt;<br /> Author: LiangJia Zhu, Stony Brook University&lt;br&gt;<br /> Author: Yi Gao, University of Alabama Birmingham&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, Stony Brook University&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the CarreraSlice interactive segmentation method. The computation is initialized using an improved GrowCut implementation and refined by an interactive, level set based segmentation algorithm, KSlice. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “CarreraSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:CarreraSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( CarreraSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> Step 6.) Initialize the segmentation using 2 labels (foreground and background), then press 'G' to run fast GrowCut.<br /> <br /> Step 5.) Select the rectangle tool(or any other painting tool).<br /> <br /> [[File:ImplicitRectangle.png|50px]]<br /> <br /> and initialize CarreraSlice in a 2D slice by drawing inside the structure of interest.<br /> <br /> [[File:KSliceInitMeningioma.png|500px]]<br /> <br /> <br /> Step 6.) Press the “C” key to copy the current initialization in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice. Once this procedure has been repeated several times, we have initialized the surface to a cube in 3D.<br /> <br /> [[File:KSliceInit3DCube.png|500px]]<br /> <br /> <br /> Step 7.) To evolve the 2D contour on a slice, hover the mouse over a 2D view plane, press “Q”.<br /> <br /> [[File:KSlice2DEvolve.png|500px]]<br /> <br /> <br /> <br /> Step 8.) Evolve the contour in 3D by pressing &quot;E&quot; to use the Chan-Vese energy.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 9.)(Used in any order) A segmenting surface may leak into undesirable areas, based purely on image data. It is the user's job to guide the evolution process. A user can provide positive input (drawing) by selecting a paint tool, painting in areas which should be part of the object of interest but are not. Or, the user can provide negative input (erasing) by pressing &quot;A&quot; (toggle label value between 0 and the originally selected label). An example of a user correction is going from <br /> <br /> [[File:KSliceNegativeInput.png|500px]]<br /> <br /> to<br /> <br /> [[File:KSliceCorrectedUI.png|500px]]<br /> <br /> Step 10.) (Used in any order) Certain image regions (depending on the energy chosen and the image itself) may be highly attractive for the evolving contour despite being incorrect according to the user's expert knowledge. He has two options. First, apply repeated input several times (soft user constraints). Second, he can press &quot;B&quot; (toggle between soft/hard constraints) to increase the weight on his inputs, essentially making them hard constraints. Further, constraints can be provided pre-emptively, by erasing/drawing in regions before a contour has reached these areas to prevent leaks in the future or expedite the evolution process, respectively. <br /> <br /> <br /> Step 11.)(Used in any order) Press &quot;F&quot; to run the contour in 3D, similarly to Step.8 but using an alternative energy, the Local Global Chan-Vese. The user can switch the energy he is using at any time.<br /> <br /> Step 12.) (Used in any order) Press &quot;U&quot; to run the contour in 3D, similarly to Step.8 but using an alternative energy, the curvature flow. The user can switch the energy he is using at any time.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 12.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOnMeningioma.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 13.) Examine the current segmentation by flipping through the 2D viewers, providing input as in Step.9 to guide the evolution. <br /> <br /> [[File:ExampleUIDuringProcess.png|500px]] <br /> <br /> <br /> <br /> Step 14.) Repeat steps 7-11 (or any subset of them) until convergence to the desired segmentation.<br /> <br /> [[File:KSliceFinalSegMeningioma.png|500px]] <br /> <br /> <br /> Step 15.) Once satisfied with the segmentation, stop CarreraSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopInteractiveSegmenter.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There are two parameters to set: the radius that sets the band around the current initialisation in which image data is considered (for Local-Global Chan-Vese energy) and the number of contour iterations. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user). The number of iterations refers to the time for which the segmenting surface is allowed to evolve before querying the user for input. A small number allows the user to catch the surface before a large error is made, reducing corrective inputs required but may be tedious/slow.<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules&diff=36891 2013-12-26T18:46:26Z

<p>Ikolesov: /* Segmentation */</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/KSliceInteractiveSegmenter|KSlice Interactive Segmenter]] (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )<br /> *[[Documentation/{{documentation/version}}/Modules/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )<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 /> <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 /> * Change quantification<br /> ** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br /> *[[Documentation/{{documentation/version}}/Modules/SNR Measurement|SNR Measurement]] (Babak Matinfar)<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 /> <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/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>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmenter&diff=35871 2013-09-20T19:44:13Z

<p>Ikolesov: </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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Georgia Institute of Technology&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, University of Alabama Birmingham&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the KSlice interactive segmentation method. It uses a data-driven automatic algorithm to process the majority of the volume. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “KSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:KSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( KSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Select the rectangle tool(or any other painting tool).<br /> <br /> [[File:ImplicitRectangle.png|50px]]<br /> <br /> and initialize KSlice in a 2D slice by drawing inside the structure of interest.<br /> <br /> [[File:KSliceInitMeningioma.png|500px]]<br /> <br /> <br /> Step 6.) Press the “C” key to copy the current initialization in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice. Once this procedure has been repeated several times, we have initialized the surface to a cube in 3D.<br /> <br /> [[File:KSliceInit3DCube.png|500px]]<br /> <br /> <br /> Step 7.) To evolve the 2D contour on a slice, hover the mouse over a 2D view plane, press “Q”.<br /> <br /> [[File:KSlice2DEvolve.png|500px]]<br /> <br /> <br /> <br /> Step 8.) Evolve the contour in 3D by pressing &quot;E&quot; to use the Chan-Vese energy.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 9.)(Used in any order) A segmenting surface may leak into undesirable areas, based purely on image data. It is the user's job to guide the evolution process. A user can provide positive input (drawing) by selecting a paint tool, painting in areas which should be part of the object of interest but are not. Or, the user can provide negative input (erasing) by pressing &quot;A&quot; (toggle label value between 0 and the originally selected label). An example of a user correction is going from <br /> <br /> [[File:KSliceNegativeInput.png|500px]]<br /> <br /> to<br /> <br /> [[File:KSliceCorrectedUI.png|500px]]<br /> <br /> Step 10.) (Used in any order) Certain image regions (depending on the energy chosen and the image itself) may be highly attractive for the evolving contour despite being incorrect according to the user's expert knowledge. He has two options. First, apply repeated input several times (soft user constraints). Second, he can press &quot;B&quot; (toggle between soft/hard constraints) to increase the weight on his inputs, essentially making them hard constraints. Further, constraints can be provided pre-emptively, by erasing/drawing in regions before a contour has reached these areas to prevent leaks in the future or expedite the evolution process, respectively. <br /> <br /> <br /> Step 11.)(Used in any order) Press &quot;F&quot; to run the contour in 3D, similarly to Step.8 but using an alternative energy, the Local Global Chan-Vese. The user can switch the energy he is using at any time.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 12.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOnMeningioma.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 13.) Examine the current segmentation by flipping through the 2D viewers, providing input as in Step.9 to guide the evolution. <br /> <br /> [[File:ExampleUIDuringProcess.png|500px]] <br /> <br /> <br /> <br /> Step 14.) Repeat steps 7-11 (or any subset of them) until convergence to the desired segmentation.<br /> <br /> [[File:KSliceFinalSegMeningioma.png|500px]] <br /> <br /> <br /> Step 15.) Once satisfied with the segmentation, stop KSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopInteractiveSegmenter.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There are two parameters to set: the radius that sets the band around the current initialisation in which image data is considered (for Local-Global Chan-Vese energy) and the number of contour iterations. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user). The number of iterations refers to the time for which the segmenting surface is allowed to evolve before querying the user for input. A small number allows the user to catch the surface before a large error is made, reducing corrective inputs required but may be tedious/slow.<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=File:StopInteractiveSegmenter.png&diff=35863 2013-09-20T10:56:02Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules&diff=35862 2013-09-20T10:49:56Z

<p>Ikolesov: /* Segmentation */</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/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/KSliceInteractiveSegmenter|KSlice Interactive Segmenter]] (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, 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) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/LASegmenter|Left Atrium Segmenter]] (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 /> * Change quantification<br /> ** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br /> *[[Documentation/{{documentation/version}}/Modules/SNR Measurement|SNR Measurement]] (Babak Matinfar)<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 /> <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 /> *[[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] (Charles Marion)<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/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>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules&diff=35861 2013-09-20T10:45:46Z

<p>Ikolesov: /* Segmentation */</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/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/KSliceSegmenter|KSlice Interactive Segmenter]] (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, 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) {{wip}}<br /> **[[Documentation/{{documentation/version}}/Modules/LASegmenter|Left Atrium Segmenter]] (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 /> * Change quantification<br /> ** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br /> *[[Documentation/{{documentation/version}}/Modules/SNR Measurement|SNR Measurement]] (Babak Matinfar)<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 /> <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 /> *[[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] (Charles Marion)<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/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>

Ikolesov https://www.slicer.org/w/index.php?title=File:VolumeRederingOnMeningioma.png&diff=35860 2013-09-20T09:56:32Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmenter&diff=35859 2013-09-20T09:53:11Z

<p>Ikolesov: </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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Georgia Institute of Technology&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, University of Alabama Birmingham&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the KSlice interactive segmentation method. It uses a data-driven automatic algorithm to process the majority of the volume. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “KSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:KSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( KSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Select the rectangle tool(or any other painting tool).<br /> <br /> [[File:ImplicitRectangle.png|50px]]<br /> <br /> and initialize KSlice in a 2D slice by drawing inside the structure of interest.<br /> <br /> [[File:KSliceInitMeningioma.png|500px]]<br /> <br /> <br /> Step 6.) Press the “C” key to copy the current initialization in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice. Once this procedure has been repeated several times, we have initialized the surface to a cube in 3D.<br /> <br /> [[File:KSliceInit3DCube.png|500px]]<br /> <br /> <br /> Step 7.) To evolve the 2D contour on a slice, hover the mouse over a 2D view plane, press “Q”.<br /> <br /> [[File:KSlice2DEvolve.png|500px]]<br /> <br /> <br /> <br /> Step 8.) Evolve the contour in 3D by pressing &quot;E&quot; to use the Chan-Vese energy.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 9.)(Used in any order) A segmenting surface may leak into undesirable areas, based purely on image data. It is the user's job to guide the evolution process. A user can provide positive input (drawing) by selecting a paint tool, painting in areas which should be part of the object of interest but are not. Or, the user can provide negative input (erasing) by pressing &quot;A&quot; (toggle label value between 0 and the originally selected label). An example of a user correction is going from <br /> <br /> [[File:KSliceNegativeInput.png|500px]]<br /> <br /> to<br /> <br /> [[File:KSliceCorrectedUI.png|500px]]<br /> <br /> Step 10.) (Used in any order) Certain image regions (depending on the energy chosen and the image itself) may be highly attractive for the evolving contour despite being incorrect according to the user's expert knowledge. He has two options. First, apply repeated input several times (soft user constraints). Second, he can press &quot;B&quot; (toggle between soft/hard constraints) to increase the weight on his inputs, essentially making them hard constraints. Further, constraints can be provided pre-emptively, by erasing/drawing in regions before a contour has reached these areas to prevent leaks in the future or expedite the evolution process, respectively. <br /> <br /> <br /> Step 11.)(Used in any order) Press &quot;F&quot; to run the contour in 3D, similarly to Step.8 but using an alternative energy, the Local Global Chan-Vese. The user can switch the energy he is using at any time.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 12.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOnMeningioma.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 13.) Examine the current segmentation by flipping through the 2D viewers, providing input as in Step.8 to guide the evolution. <br /> <br /> [[File:ExampleUIDuringProcess.png|500px]] <br /> <br /> <br /> <br /> Step 14.) Repeat steps 7-11 (or any subset of them) until convergence to the desired segmentation.<br /> <br /> [[File:KSliceFinalSegMeningioma.png|500px]] <br /> <br /> <br /> Step 15.) Once satisfied with the segmentation, stop KSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopKSlice.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There are two parameters to set: the radius that sets the band around the current initialisation in which image data is considered (for Local-Global Chan-Vese energy) and the number of contour iterations. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user). The number of iterations refers to the time for which the segmenting surface is allowed to evolve before querying the user for input. A small number allows the user to catch the surface before a large error is made, reducing corrective inputs required but may be tedious/slow.<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmenter&diff=35858 2013-09-20T09:44:15Z

<p>Ikolesov: </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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Georgia Institute of Technology&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, University of Alabama Birmingham&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the KSlice interactive segmentation method. It uses a data-driven automatic algorithm to process the majority of the volume. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “KSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:KSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( KSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Select the rectangle tool(or any other painting tool).<br /> <br /> [[File:ImplicitRectangle.png|50px]]<br /> <br /> and initialize KSlice in a 2D slice by drawing inside the structure of interest.<br /> <br /> [[File:KSliceInitMeningioma.png|500px]]<br /> <br /> <br /> Step 6.) Press the “C” key to copy the current initialization in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice. Once this procedure has been repeated several times, we have initialized the surface to a cube in 3D.<br /> <br /> [[File:KSliceInit3DCube.png|500px]]<br /> <br /> <br /> Step 7.) To evolve the 2D contour on a slice, hover the mouse over a 2D view plane, press “Q”.<br /> <br /> [[File:KSlice2DEvolve.png|500px]]<br /> <br /> <br /> <br /> Step 8.) Evolve the contour in 3D by pressing &quot;E&quot; to use the Chan-Vese energy.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 9.)(Used in any order) A segmenting surface may leak into undesirable areas, based purely on image data. It is the user's job to guide the evolution process. A user can provide positive input (drawing) by selecting a paint tool, painting in areas which should be part of the object of interest but are not. Or, the user can provide negative input (erasing) by pressing &quot;A&quot; (toggle label value between 0 and the originally selected label). An example of a user correction is going from <br /> <br /> [[File:KSliceNegativeInput.png|500px]]<br /> <br /> to<br /> <br /> [[File:KSliceCorrectedUI.png|500px]]<br /> <br /> Step 10.) (Used in any order) Certain image regions (depending on the energy chosen and the image itself) may be highly attractive for the evolving contour despite being incorrect according to the user's expert knowledge. He has two options. First, apply repeated input several times (soft user constraints). Second, he can press &quot;B&quot; (toggle between soft/hard constraints) to increase the weight on his inputs, essentially making them hard constraints. Further, constraints can be provided pre-emptively, by erasing/drawing in regions before a contour has reached these areas to prevent leaks in the future or expedite the evolution process, respectively. <br /> <br /> <br /> Step 11.)(Used in any order) Press &quot;F&quot; to run the contour in 3D, similarly to Step.8 but using an alternative energy, the Local Global Chan-Vese. The user can switch the energy he is using at any time.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 12.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOn.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 13.) Examine the current segmentation by flipping through the 2D viewers, providing input as in Step.8 to guide the evolution. <br /> <br /> [[File:ExampleUIDuringProcess.png|500px]] <br /> <br /> <br /> <br /> Step 14.) Repeat steps 7-11 (or any subset of them) until convergence to the desired segmentation.<br /> <br /> [[File:KSliceFinalSegMeningioma.png|500px]] <br /> <br /> <br /> Step 15.) Once satisfied with the segmentation, stop KSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopKSlice.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There are two parameters to set: the radius that sets the band around the current initialisation in which image data is considered (for Local-Global Chan-Vese energy) and the number of contour iterations. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user). The number of iterations refers to the time for which the segmenting surface is allowed to evolve before querying the user for input. A small number allows the user to catch the surface before a large error is made, reducing corrective inputs required but may be tedious/slow.<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmenter&diff=35857 2013-09-20T09:30:40Z

<p>Ikolesov: </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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Georgia Institute of Technology&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, University of Alabama Birmingham&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the KSlice interactive segmentation method. It uses a data-driven automatic algorithm to process the majority of the volume. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “KSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:KSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( KSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Select the rectangle tool(or any other painting tool).<br /> <br /> [[File:ImplicitRectangle.png|50px]]<br /> <br /> and initialize KSlice in a 2D slice by drawing inside the structure of interest.<br /> <br /> [[File:KSliceInitMeningioma.png|500px]]<br /> <br /> <br /> Step 6.) Press the “C” key to copy the current initialization in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice. Once this procedure has been repeated several times, we have initialized the surface to a cube in 3D.<br /> <br /> [[File:KSliceInit3DCube.png|500px]]<br /> <br /> <br /> Step 7.) To evolve the 2D contour on a slice, hover the mouse over a 2D view plane, press “Q”.<br /> <br /> [[File:KSlice2DEvolve.png|500px]]<br /> <br /> Step 8.) A segmenting surface may leak into undesirable areas, based purely on image data. It is the user's job to guide the evolution process. A user can provide positive input (drawing) by selecting a paint tool, painting in areas which should be part of the object of interest but are not. Or, the user can provide negative input (erasing) by pressing &quot;A&quot; (toggle label value between 0 and the originally selected label). An example of a user correction is going from <br /> <br /> [[File:KSliceNegativeInput.png|500px]]<br /> <br /> to<br /> <br /> [[File:KSliceCorrectedUI.png|500px]]<br /> <br /> (Note: Certain image regions (depending on the energy chosen and the image itself) may be highly attractive for the evolving contour despite being incorrect according to the user's expert knowledge. He has two options. First, apply repeated input several times (soft user constraints). Second, he can press &quot;B&quot; (toggle between soft/hard constraints) to increase the weight on his inputs, essentially making them hard constraints. Further, constraints can be provided preemptively, by erasing/drawing in regions before a contour has reached these areas to prevent leaks in the future or expedite the evolution process, respectively. <br /> <br /> Step 9.) Evolve the contour in 3D by pressing &quot;E&quot; to use the Chan-Vese energy.<br /> <br /> <br /> <br /> Step 10.) Examine the current segmentation by flipping through the 2D viewers, providing input as in Step.8 to guide the evolution. <br /> <br /> [[File:ExampleUIDuringProcess.png|500px]] <br /> <br /> Step 11.) Repeat steps 9-10 until convergence to the desired segmentation.<br /> <br /> [[File:KSliceFinalSegMeningioma.png|500px]] <br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 10.)(Used in any order) Press the “A” key to change drawing modes (between Draw/Delete label). Thus, if the user's expert knowledge of anatomy does not agree with the current segmentation results, he adds negative input by erasing a label. By deleting in the same area multiple times, the user input is accumulated and this guiding signal forces the changes to become persistent<br /> <br /> [[File:DeleteLabel.png|500px]]<br /> <br /> <br /> Step 11.)(Used in any order) Alternatively, a user can press “A” again to return to drawing. If a contour is not reaching an area that is, in fact, part of the structure of interest, the user can add positive input by painting this area<br /> <br /> [[File:DrawLabel.png|500px]]<br /> <br /> <br /> Step 12.)(Used in any order) Evolve the contour with the changed user input, and new initialization<br /> <br /> [[File:EvolveAfterUserInput.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 13.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOn.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 14.) Evolution in 3D is done by pressing the “W” key<br /> <br /> [[File:Result3DSegmentation.png|500px]]<br /> <br /> Step 15.) Once satisfies with the segmentation, stop KSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopKSlice.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There are two parameters to set: the radius that sets the band around the current initialisation in which image data is considered (for Local-Global Chan-Vese energy) and the number of contour iterations. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user). The number of iterations refers to the time for which the segmenting surface is allowed to evolve before querying the user for input. A small number allows the user to catch the surface before a large error is made, reducing corrective inputs required but may be tedious/slow.<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=File:ImplicitRectangle.png&diff=35856 2013-09-20T09:29:47Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmenter&diff=35855 2013-09-20T09:28:19Z

<p>Ikolesov: </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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Georgia Institute of Technology&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, University of Alabama Birmingham&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the KSlice interactive segmentation method. It uses a data-driven automatic algorithm to process the majority of the volume. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “KSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:KSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( KSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Select the rectangle tool(or any other painting tool).<br /> <br /> [[File:ImplicitRectangle.png|50px]]<br /> <br /> and initialize KSlice in a 2D slice by drawing inside the structure of interest.<br /> <br /> [[File:KSliceInitMeningioma.png|500px]]<br /> <br /> <br /> Step 6.) Press the “C” key to copy the current initialization in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice. Once this procedure has been repeated several times, we have intialized the surface to a cube in 3D.<br /> <br /> [[File:KSliceInit3DCube.png|500px]]<br /> <br /> <br /> Step 7.) To evolve the 2D contour on a slice, hover the mouse over a 2D view plane, press “Q”.<br /> <br /> [[File:KSlice2DEvolve.png|500px]]<br /> <br /> Step 8.) A segmenting surface may leak into undesirable areas, based purely on image data. It is the user's job to guide the evolution process. A user can provide positive input (drawing) by selecting a paint tool, painting in areas which should be part of the object of interest but are not. Or, the user can provide negative input (erasing) by pressing &quot;A&quot; (toggle label value between 0 and the originally selected label). An example of a user correction is going from <br /> <br /> [[File:KSliceNegativeInput.png|500px]]<br /> <br /> to<br /> <br /> [[File:KSliceCorrectedUI.png|500px]]<br /> <br /> (Note: Certain image regions (depending on the energy chosen and the image itself) may be highly attractive for the evolving contour despite being incorrect according to the user's expert knowledge. He has two options. First, apply repeated input several times (soft user constraints). Second, he can press &quot;B&quot; (toggle between soft/hard constraints) to increase the weight on his inputs, essentially making them hard constraints. Further, constraints can be provided preemptively, by erasing/drawing in regions before a contour has reached these areas to prevent leaks in the future or expedite the evolution process, respectively. <br /> <br /> Step 9.) Evolve the contour in 3D by pressing &quot;E&quot; to use the Chan-Vese energy.<br /> <br /> <br /> <br /> Step 10.) Examine the current segmentation by flipping through the 2D viewers, providing input as in Step.8 to guide the evolution. <br /> <br /> [[File:ExampleUIDuringProcess.png|500px]] <br /> <br /> Step 11.) Repeat steps 9-10 until convergence to the desired segmentation.<br /> <br /> [[File:KSliceFinalSegMeningioma.png|500px]] <br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 10.)(Used in any order) Press the “A” key to change drawing modes (between Draw/Delete label). Thus, if the user's expert knowledge of anatomy does not agree with the current segmentation results, he adds negative input by erasing a label. By deleting in the same area multiple times, the user input is accumulated and this guiding signal forces the changes to become persistent<br /> <br /> [[File:DeleteLabel.png|500px]]<br /> <br /> <br /> Step 11.)(Used in any order) Alternatively, a user can press “A” again to return to drawing. If a contour is not reaching an area that is, in fact, part of the structure of interest, the user can add positive input by painting this area<br /> <br /> [[File:DrawLabel.png|500px]]<br /> <br /> <br /> Step 12.)(Used in any order) Evolve the contour with the changed user input, and new initialization<br /> <br /> [[File:EvolveAfterUserInput.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 13.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOn.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 14.) Evolution in 3D is done by pressing the “W” key<br /> <br /> [[File:Result3DSegmentation.png|500px]]<br /> <br /> Step 15.) Once satisfies with the segmentation, stop KSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopKSlice.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There are two parameters to set: the radius that sets the band around the current initialisation in which image data is considered (for Local-Global Chan-Vese energy) and the number of contour iterations. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user). The number of iterations refers to the time for which the segmenting surface is allowed to evolve before querying the user for input. A small number allows the user to catch the surface before a large error is made, reducing corrective inputs required but may be tedious/slow.<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=File:TurnOnSlices3DMeningioma.png&diff=35854 2013-09-20T09:22:17Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:StartEditorMeningioma.png&diff=35853 2013-09-20T09:21:20Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:StartBotMeningioma.png&diff=35852 2013-09-20T09:20:41Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:LoadMeningioma.png&diff=35851 2013-09-20T09:19:56Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:KSliceOne3DEvolutionCV.png&diff=35850 2013-09-20T09:19:12Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:KSliceNegativeInput.png&diff=35849 2013-09-20T09:18:41Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:KSliceInitMeningioma.png&diff=35848 2013-09-20T09:16:35Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:KSliceInit3DCube.png&diff=35847 2013-09-20T09:13:26Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:KSliceFinalSegMeningioma.png&diff=35846 2013-09-20T09:12:08Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:KSliceCorrectedUI.png&diff=35845 2013-09-20T09:09:56Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:KSlice2DEvolve.png&diff=35844 2013-09-20T09:08:33Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:ExampleUIDuringProcess.png&diff=35842 2013-09-19T20:08:31Z

<p>Ikolesov: uploaded a new version of &quot;File:ExampleUIDuringProcess.png&quot;</p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=File:ExampleUIDuringProcess.png&diff=35841 2013-09-19T20:05:45Z

<p>Ikolesov: </p> <hr /> <div></div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmenter&diff=35840 2013-09-19T20:03:02Z

<p>Ikolesov: </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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Georgia Institute of Technology&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, University of Alabama Birmingham&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the KSlice interactive segmentation method. It uses a data-driven automatic algorithm to process the majority of the volume. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “KSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:KSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( KSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Select the rectangle tool(or any other painting tool).<br /> <br /> [[File:RectangleEffect.png|50px]]<br /> <br /> and initialize KSlice in a 2D slice by drawing inside the structure of interest.<br /> <br /> [[File:KSliceInitMeningioma.png|500px]]<br /> <br /> <br /> Step 6.) Press the “C” key to copy the current initialization in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice. Once this procedure has been repeated several times, we have intialized the surface to a cube in 3D.<br /> <br /> [[File:KSliceInit3DCube.png|500px]]<br /> <br /> <br /> Step 7.) To evolve the 2D contour on a slice, hover the mouse over a 2D view plane, press “Q”.<br /> <br /> [[File:KSlice2DEvolve.png|500px]]<br /> <br /> Step 8.) A segmenting surface may leak into undesirable areas, based purely on image data. It is the user's job to guide the evolution process. A user can provide positive input (drawing) by selecting a paint tool, painting in areas which should be part of the object of interest but are not. Or, the user can provide negative input (erasing) by pressing &quot;A&quot; (toggle label value between 0 and the originally selected label). An example of a user correction is going from <br /> <br /> [[File:KSliceNegativeInput.png|500px]]<br /> <br /> to<br /> <br /> [[File:KSliceCorrectedUI.png|500px]]<br /> <br /> (Note: Certain image regions (depending on the energy chosen and the image itself) may be highly attractive for the evolving contour despite being incorrect according to the user's expert knowledge. He has two options. First, apply repeated input several times (soft user constraints). Second, he can press &quot;B&quot; (toggle between soft/hard constraints) to increase the weight on his inputs, essentially making them hard constraints. Further, constraints can be provided preemptively, by erasing/drawing in regions before a contour has reached these areas to prevent leaks in the future or expedite the evolution process, respectively. <br /> <br /> Step 9.) Evolve the contour in 3D by pressing &quot;E&quot; to use the Chan-Vese energy.<br /> <br /> <br /> <br /> Step 10.) Examine the current segmentation by flipping through the 2D viewers, providing input as in Step.8 to guide the evolution. <br /> <br /> [[File:ExampleUIDuringProcess.png|500px]] <br /> <br /> Step 11.) Repeat steps 9-10 until convergence to the desired segmentation.<br /> <br /> [[File:KSliceFinalSegMeningioma.png|500px]] <br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 10.)(Used in any order) Press the “A” key to change drawing modes (between Draw/Delete label). Thus, if the user's expert knowledge of anatomy does not agree with the current segmentation results, he adds negative input by erasing a label. By deleting in the same area multiple times, the user input is accumulated and this guiding signal forces the changes to become persistent<br /> <br /> [[File:DeleteLabel.png|500px]]<br /> <br /> <br /> Step 11.)(Used in any order) Alternatively, a user can press “A” again to return to drawing. If a contour is not reaching an area that is, in fact, part of the structure of interest, the user can add positive input by painting this area<br /> <br /> [[File:DrawLabel.png|500px]]<br /> <br /> <br /> Step 12.)(Used in any order) Evolve the contour with the changed user input, and new initialization<br /> <br /> [[File:EvolveAfterUserInput.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 13.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOn.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 14.) Evolution in 3D is done by pressing the “W” key<br /> <br /> [[File:Result3DSegmentation.png|500px]]<br /> <br /> Step 15.) Once satisfies with the segmentation, stop KSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopKSlice.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There are two parameters to set: the radius that sets the band around the current initialisation in which image data is considered (for Local-Global Chan-Vese energy) and the number of contour iterations. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user). The number of iterations refers to the time for which the segmenting surface is allowed to evolve before querying the user for input. A small number allows the user to catch the surface before a large error is made, reducing corrective inputs required but may be tedious/slow.<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmenter&diff=35839 2013-09-19T20:02:16Z

<p>Ikolesov: </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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Georgia Institute of Technology&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, University of Alabama Birmingham&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the KSlice interactive segmentation method. It uses a data-driven automatic algorithm to process the majority of the volume. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “KSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:KSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( KSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Select the rectangle tool(or any other painting tool).<br /> <br /> [[File:RectangleEffect.png|50px]]<br /> <br /> and initialize KSlice in a 2D slice by drawing inside the structure of interest.<br /> <br /> [[File:KSliceInitMeningioma.png|500px]]<br /> <br /> <br /> Step 6.) Press the “C” key to copy the current initialization in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice. Once this procedure has been repeated several times, we have intialized the surface to a cube in 3D.<br /> <br /> [[File:KSliceInit3DCube.png|500px]]<br /> <br /> <br /> Step 7.) To evolve the 2D contour on a slice, hover the mouse over a 2D view plane, press “Q”.<br /> <br /> [[File:KSlice2DEvolve.png|500px]]<br /> <br /> Step 8.) A segmenting surface may leak into undesirable areas, based purely on image data. It is the user's job to guide the evolution process. A user can provide positive input (drawing) by selecting a paint tool, painting in areas which should be part of the object of interest but are not. Or, the user can provide negative input (erasing) by pressing &quot;A&quot; (toggle label value between 0 and the originally selected label). An example of a user correction is going from <br /> <br /> [[File:KSliceNegativeInput.png|500px]]<br /> <br /> to<br /> <br /> [[File:KSliceCorrectedUI.png|500px]]<br /> <br /> (Note: Certain image regions (depending on the energy chosen and the image itself) may be highly attractive for the evolving contour despite being incorrect according to the user's expert knowledge. He has two options. First, apply repeated input several times (soft user constraints). Second, he can press &quot;B&quot; (toggle between soft/hard constraints) to increase the weight on his inputs, essentially making them hard constraints. Further, constraints can be provided preemptively, by erasing/drawing in regions before a contour has reached these areas to prevent leaks in the future or expedite the evolution process, respectively. <br /> <br /> Step 9.) Evolve the contour in 3D by pressing &quot;E&quot; to use the Chan-Vese energy.<br /> <br /> <br /> <br /> Step 10.) Examine the current segmentation by flipping through the 2D viewers, providing input as in Step.8 to guide the evolution. <br /> <br /> [[File:ExampleUIDuringProcess.png|500px]] <br /> <br /> Step 11.) Repeat steps 9-10 until convergence to the desired segmentation.<br /> [[File:KSliceFinalSegMeningioma.png|500px]] <br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 10.)(Used in any order) Press the “A” key to change drawing modes (between Draw/Delete label). Thus, if the user's expert knowledge of anatomy does not agree with the current segmentation results, he adds negative input by erasing a label. By deleting in the same area multiple times, the user input is accumulated and this guiding signal forces the changes to become persistent<br /> <br /> [[File:DeleteLabel.png|500px]]<br /> <br /> <br /> Step 11.)(Used in any order) Alternatively, a user can press “A” again to return to drawing. If a contour is not reaching an area that is, in fact, part of the structure of interest, the user can add positive input by painting this area<br /> <br /> [[File:DrawLabel.png|500px]]<br /> <br /> <br /> Step 12.)(Used in any order) Evolve the contour with the changed user input, and new initialization<br /> <br /> [[File:EvolveAfterUserInput.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 13.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOn.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 14.) Evolution in 3D is done by pressing the “W” key<br /> <br /> [[File:Result3DSegmentation.png|500px]]<br /> <br /> Step 15.) Once satisfies with the segmentation, stop KSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopKSlice.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There are two parameters to set: the radius that sets the band around the current initialisation in which image data is considered (for Local-Global Chan-Vese energy) and the number of contour iterations. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user). The number of iterations refers to the time for which the segmenting surface is allowed to evolve before querying the user for input. A small number allows the user to catch the surface before a large error is made, reducing corrective inputs required but may be tedious/slow.<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmenter&diff=35838 2013-09-19T19:49:59Z

<p>Ikolesov: </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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Georgia Institute of Technology&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, University of Alabama Birmingham&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the KSlice interactive segmentation method. It uses a data-driven automatic algorithm to process the majority of the volume. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “KSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:KSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( KSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Select the rectangle tool(or any other painting tool).<br /> <br /> [[File:RectangleEffect.png|50px]]<br /> <br /> and initialize KSlice in a 2D slice by drawing inside the structure of interest.<br /> <br /> [[File:KSliceInitMeningioma.png|500px]]<br /> <br /> <br /> Step 6.) Press the “C” key to copy the current initialization in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice. Once this procedure has been repeated several times, we have intialized the surface to a cube in 3D.<br /> <br /> [[File:KSliceInit3DCube.png|500px]]<br /> <br /> <br /> Step 7.) To evolve the 2D contour on a slice, hover the mouse over a 2D view plane, press “Q”.<br /> <br /> [[File:KSlice2DEvolve.png|500px]]<br /> <br /> Step 8.) A segmenting surface may leak into undesirable areas, based purely on image data. It is the user's job to guide the evolution process. A user can provide positive input (drawing) by selecting a paint tool, painting in areas which should be part of the object of interest but are not. Or, the user can provide negative input (erasing) by pressing &quot;A&quot; (toggle label value between 0 and the originally selected label). An example of a user correction is going from <br /> <br /> [[File:KSliceNegativeInput.png|500px]]<br /> <br /> to<br /> <br /> [[File:KSliceCorrectedUI.png|500px]]<br /> <br /> (Note: Certain image regions (depending on the energy chosen and the image itself) may be highly attractive for the evolving contour despite being incorrect according to the user's expert knowledge. He has two options. First, apply repeated input several times (soft user constraints). Second, he can press &quot;B&quot; (toggle between soft/hard constraints) to increase the weight on his inputs, essentially making them hard constraints. Further, constraints can be provided preemptively, by erasing/drawing in regions before a contour has reached these areas to prevent leaks in the future or expedite the evolution process, respectively. <br /> <br /> Step 9.) Evolve the contour in 3D by pressing &quot;E&quot; to use the Chan-Vese energy.<br /> <br /> <br /> <br /> Step 10.) Examine the current segmentation by flipping through the 2D viewers, providing input as in Step.8 to guide the evolution. <br /> <br /> [[File:ExampleUIDuringProcess.png|500px]] <br /> <br /> Step 11.) Repeat steps 9-10 until convergence to the desired segmentation.<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 10.)(Used in any order) Press the “A” key to change drawing modes (between Draw/Delete label). Thus, if the user's expert knowledge of anatomy does not agree with the current segmentation results, he adds negative input by erasing a label. By deleting in the same area multiple times, the user input is accumulated and this guiding signal forces the changes to become persistent<br /> <br /> [[File:DeleteLabel.png|500px]]<br /> <br /> <br /> Step 11.)(Used in any order) Alternatively, a user can press “A” again to return to drawing. If a contour is not reaching an area that is, in fact, part of the structure of interest, the user can add positive input by painting this area<br /> <br /> [[File:DrawLabel.png|500px]]<br /> <br /> <br /> Step 12.)(Used in any order) Evolve the contour with the changed user input, and new initialization<br /> <br /> [[File:EvolveAfterUserInput.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 13.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOn.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 14.) Evolution in 3D is done by pressing the “W” key<br /> <br /> [[File:Result3DSegmentation.png|500px]]<br /> <br /> Step 15.) Once satisfies with the segmentation, stop KSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopKSlice.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There is one parameter to set: the radius that sets the band around the current initialisation in which image data is considered. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user)<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmenter&diff=35832 2013-09-19T19:17:07Z

<p>Ikolesov: </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 /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Georgia Institute of Technology&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, University of Alabama Birmingham&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the KSlice interactive segmentation method. It uses a data-driven automatic algorithm to process the majority of the volume. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadMeningioma.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditorMeningioma.png|500px]]<br /> <br /> <br /> Step 3.) Select the “KSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:KSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter, the &quot;Number of Iterations&quot; and press the “Start Interactive Segmentor” button ( KSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBotMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3DMeningioma.png|500px]]<br /> <br /> <br /> Step 5.) Select the rectangle tool(or any other painting tool).<br /> <br /> [[File:RectangleEffect.png|50px]]<br /> <br /> and initialize KSlice in a 2D slice by drawing inside the structure of interest.<br /> <br /> [[File:KSliceInitMeningioma.png|500px]]<br /> <br /> <br /> Step 6.) Press the “C” key to copy the current initialization in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice. Once this procedure has been repeated several times, we have intialized the surface to a cube in 3D.<br /> <br /> [[File:KSliceInit3DCube.png|500px]]<br /> <br /> <br /> Step 7.) To evolve the 2D contour on a slice, hover the mouse over a 2D view plane, press “Q”.<br /> <br /> [[File:KSlice2DEvolve.png|500px]]<br /> <br /> <br /> Step 9.) Hover mouse over the yellow, then green slices and repeat (as many times as desired) Steps 6-8<br /> <br /> [[File:SegmentAllSlices.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 10.)(Used in any order) Press the “A” key to change drawing modes (between Draw/Delete label). Thus, if the user's expert knowledge of anatomy does not agree with the current segmentation results, he adds negative input by erasing a label. By deleting in the same area multiple times, the user input is accumulated and this guiding signal forces the changes to become persistent<br /> <br /> [[File:DeleteLabel.png|500px]]<br /> <br /> <br /> Step 11.)(Used in any order) Alternatively, a user can press “A” again to return to drawing. If a contour is not reaching an area that is, in fact, part of the structure of interest, the user can add positive input by painting this area<br /> <br /> [[File:DrawLabel.png|500px]]<br /> <br /> <br /> Step 12.)(Used in any order) Evolve the contour with the changed user input, and new initialization<br /> <br /> [[File:EvolveAfterUserInput.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 13.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOn.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 14.) Evolution in 3D is done by pressing the “W” key<br /> <br /> [[File:Result3DSegmentation.png|500px]]<br /> <br /> Step 15.) Once satisfies with the segmentation, stop KSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopKSlice.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There is one parameter to set: the radius that sets the band around the current initialisation in which image data is considered. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user)<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmenter&diff=31598 2013-05-12T20:11:48Z

<p>Ikolesov: </p> <hr /> <div>&lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Georgia Institute of Technology&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, University of Alabama Birmingham&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> Contributor2: Karl Fritscher (BWH &amp; MGH)&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the KSlice interactive segmentation method. It uses a data-driven automatic algorithm to process the majority of the volume. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadData.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditor.png|500px]]<br /> <br /> <br /> Step 3.) Select the “KSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:KSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter and press the “Start Interactive Segmentor” button ( KSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBot.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3D.png|500px]]<br /> <br /> <br /> Step 5.) Select the “PaintEffect” tool <br /> (green circle, inside the esophagus in this example)<br /> <br /> [[File:Paint.png|50px]]<br /> <br /> and initialize KSlice by drawing inside the structure of interest<br /> <br /> [[File:KSliceInit.png|500px]]<br /> <br /> Step 6.) Hover the mouse over a slice view (we focus on the “Red” slice first, here) and press the “Q” key to evolve a 2D active contour in this plane<br /> <br /> [[File:Segment2D.png|500px]]<br /> <br /> <br /> Step 7.) Press the “C” key to copy the current segmentation in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice<br /> <br /> [[File:CopyPasteSlice.png|500px]]<br /> <br /> <br /> Step 8.) Evolve the 2D contour on this slice by pressing “Q” <br /> <br /> [[File:Segment2DAfterPaste.png|500px]]<br /> <br /> <br /> Step 9.) Hover mouse over the yellow, then green slices and repeat (as many times as desired) Steps 6-8<br /> <br /> [[File:SegmentAllSlices.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 10.)(Used in any order) Press the “A” key to change drawing modes (between Draw/Delete label). Thus, if the user's expert knowledge of anatomy does not agree with the current segmentation results, he adds negative input by erasing a label. By deleting in the same area multiple times, the user input is accumulated and this guiding signal forces the changes to become persistent<br /> <br /> [[File:DeleteLabel.png|500px]]<br /> <br /> <br /> Step 11.)(Used in any order) Alternatively, a user can press “A” again to return to drawing. If a contour is not reaching an area that is, in fact, part of the structure of interest, the user can add positive input by painting this area<br /> <br /> [[File:DrawLabel.png|500px]]<br /> <br /> <br /> Step 12.)(Used in any order) Evolve the contour with the changed user input, and new initialization<br /> <br /> [[File:EvolveAfterUserInput.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 13.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOn.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 14.) Evolution in 3D is done by pressing the “W” key<br /> <br /> [[File:Result3DSegmentation.png|500px]]<br /> <br /> Step 15.) Once satisfies with the segmentation, stop KSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopKSlice.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There is one parameter to set: the radius that sets the band around the current initialisation in which image data is considered. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user)<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules&diff=31597 2013-05-12T20:10:39Z

<p>Ikolesov: /* Segmentation */</p> <hr /> <div>=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/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/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) [[image:UnderConstruction.png|tumb|10px]]<br /> **Vector Demon Registration (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)<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/KSliceInteractiveSegmenter|KSlice Interactive Segmenter]] (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, 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 /> <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 /> * Change quantification<br /> ** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br /> <br /> ==Diffusion== <br /> *DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Tractography<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]<br /> *Utilities<br /> **[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Data Conversion<br /> **[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol) <br /> **[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)<br /> <br /> ==IGT==<br /> *[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) <br /> *[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *Arithmetic <br /> **[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] <br /> **[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Surface Models==<br /> *[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Converters==<br /> *[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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 /> [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Endoscopy==<br /> *[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br /> <br /> ==[[image:UnderConstruction.png|tumb|10px]] Work in Progress [[image:UnderConstruction.png|tumb|10px]]==<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *Registration<br /> **[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett)[[image:UnderConstruction.png|tumb|10px]]<br /> &lt;!--<br /> **[[Documentation/{{documentation/version}}/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> --&gt;<br /> *Segmentation<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules&diff=31596 2013-05-12T20:08:39Z

<p>Ikolesov: /* Segmentation */</p> <hr /> <div>=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/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/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) [[image:UnderConstruction.png|tumb|10px]]<br /> **Vector Demon Registration (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)<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/KSliceInteractiveSegmenter|KSlice Interactive Segmenter]] (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, 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 /> <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 /> * Change quantification<br /> ** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br /> <br /> ==Diffusion== <br /> *DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Tractography<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]<br /> *Utilities<br /> **[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Data Conversion<br /> **[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol) <br /> **[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)<br /> <br /> ==IGT==<br /> *[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) <br /> *[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *Arithmetic <br /> **[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] <br /> **[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Surface Models==<br /> *[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Converters==<br /> *[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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 /> [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Endoscopy==<br /> *[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br /> <br /> ==[[image:UnderConstruction.png|tumb|10px]] Work in Progress [[image:UnderConstruction.png|tumb|10px]]==<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *Registration<br /> **[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett)[[image:UnderConstruction.png|tumb|10px]]<br /> &lt;!--<br /> **[[Documentation/{{documentation/version}}/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> --&gt;<br /> *Segmentation<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmenter&diff=31594 2013-05-12T20:08:03Z

<p>Ikolesov: moved Documentation/Nightly/Modules/KSliceInteractiveSegmentor to Documentation/Nightly/Modules/KSliceInteractiveSegmenter:&amp;#32;wrong spelling</p> <hr /> <div>&lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Georgia Institute of Technology&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, University of Alabama Birmingham&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the KSlice interactive segmentation method. It uses a data-driven automatic algorithm to process the majority of the volume. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadData.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditor.png|500px]]<br /> <br /> <br /> Step 3.) Select the “KSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:KSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter and press the “Start Interactive Segmentor” button ( KSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBot.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3D.png|500px]]<br /> <br /> <br /> Step 5.) Select the “PaintEffect” tool <br /> (green circle, inside the esophagus in this example)<br /> <br /> [[File:Paint.png|50px]]<br /> <br /> and initialize KSlice by drawing inside the structure of interest<br /> <br /> [[File:KSliceInit.png|500px]]<br /> <br /> Step 6.) Hover the mouse over a slice view (we focus on the “Red” slice first, here) and press the “Q” key to evolve a 2D active contour in this plane<br /> <br /> [[File:Segment2D.png|500px]]<br /> <br /> <br /> Step 7.) Press the “C” key to copy the current segmentation in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice<br /> <br /> [[File:CopyPasteSlice.png|500px]]<br /> <br /> <br /> Step 8.) Evolve the 2D contour on this slice by pressing “Q” <br /> <br /> [[File:Segment2DAfterPaste.png|500px]]<br /> <br /> <br /> Step 9.) Hover mouse over the yellow, then green slices and repeat (as many times as desired) Steps 6-8<br /> <br /> [[File:SegmentAllSlices.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 10.)(Used in any order) Press the “A” key to change drawing modes (between Draw/Delete label). Thus, if the user's expert knowledge of anatomy does not agree with the current segmentation results, he adds negative input by erasing a label. By deleting in the same area multiple times, the user input is accumulated and this guiding signal forces the changes to become persistent<br /> <br /> [[File:DeleteLabel.png|500px]]<br /> <br /> <br /> Step 11.)(Used in any order) Alternatively, a user can press “A” again to return to drawing. If a contour is not reaching an area that is, in fact, part of the structure of interest, the user can add positive input by painting this area<br /> <br /> [[File:DrawLabel.png|500px]]<br /> <br /> <br /> Step 12.)(Used in any order) Evolve the contour with the changed user input, and new initialization<br /> <br /> [[File:EvolveAfterUserInput.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 13.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOn.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 14.) Evolution in 3D is done by pressing the “W” key<br /> <br /> [[File:Result3DSegmentation.png|500px]]<br /> <br /> Step 15.) Once satisfies with the segmentation, stop KSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopKSlice.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There is one parameter to set: the radius that sets the band around the current initialisation in which image data is considered. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user)<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmentor&diff=31595 2013-05-12T20:08:03Z

<p>Ikolesov: moved Documentation/Nightly/Modules/KSliceInteractiveSegmentor to Documentation/Nightly/Modules/KSliceInteractiveSegmenter:&amp;#32;wrong spelling</p> <hr /> <div>#REDIRECT [[Documentation/Nightly/Modules/KSliceInteractiveSegmenter]]</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules&diff=31593 2013-05-12T20:03:02Z

<p>Ikolesov: /* Segmentation */</p> <hr /> <div>=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/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/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) [[image:UnderConstruction.png|tumb|10px]]<br /> **Vector Demon Registration (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)<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/KSliceInteractiveSegmentor|KSlice Interactive Segmenter]] (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, 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 /> <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 /> * Change quantification<br /> ** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br /> <br /> ==Diffusion== <br /> *DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Tractography<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]<br /> *Utilities<br /> **[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Data Conversion<br /> **[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol) <br /> **[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)<br /> <br /> ==IGT==<br /> *[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) <br /> *[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *Arithmetic <br /> **[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] <br /> **[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Surface Models==<br /> *[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Converters==<br /> *[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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 /> [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Endoscopy==<br /> *[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br /> <br /> ==[[image:UnderConstruction.png|tumb|10px]] Work in Progress [[image:UnderConstruction.png|tumb|10px]]==<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *Registration<br /> **[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett)[[image:UnderConstruction.png|tumb|10px]]<br /> &lt;!--<br /> **[[Documentation/{{documentation/version}}/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> --&gt;<br /> *Segmentation<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules&diff=31592 2013-05-12T20:02:17Z

<p>Ikolesov: /* Segmentation */</p> <hr /> <div>=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/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/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) [[image:UnderConstruction.png|tumb|10px]]<br /> **Vector Demon Registration (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)<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/KSliceInteractiveSegmentor]] (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, 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 /> <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 /> * Change quantification<br /> ** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br /> <br /> ==Diffusion== <br /> *DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Tractography<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]<br /> *Utilities<br /> **[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Data Conversion<br /> **[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol) <br /> **[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)<br /> <br /> ==IGT==<br /> *[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) <br /> *[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *Arithmetic <br /> **[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] <br /> **[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Surface Models==<br /> *[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Converters==<br /> *[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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 /> [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Endoscopy==<br /> *[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br /> <br /> ==[[image:UnderConstruction.png|tumb|10px]] Work in Progress [[image:UnderConstruction.png|tumb|10px]]==<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *Registration<br /> **[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett)[[image:UnderConstruction.png|tumb|10px]]<br /> &lt;!--<br /> **[[Documentation/{{documentation/version}}/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> --&gt;<br /> *Segmentation<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules&diff=31591 2013-05-12T20:01:42Z

<p>Ikolesov: /* Segmentation */</p> <hr /> <div>=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/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/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) [[image:UnderConstruction.png|tumb|10px]]<br /> **Vector Demon Registration (Hans Johnson)<br /> **[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue)<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/KSliceInteractiveSegmentor (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, 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 /> <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 /> * Change quantification<br /> ** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br /> <br /> ==Diffusion== <br /> *DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Tractography<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/UKFTractography|UKF Tractography]]<br /> *Utilities<br /> **[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) <br /> **[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br /> *Data Conversion<br /> **[[Documentation/{{documentation/version}}/Modules/DTIImport|DTIImport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol) <br /> **[[Documentation/{{documentation/version}}/Modules/DTIExport|DTIExport]][[image:UnderConstruction.png|tumb|10px]] (Sonia Pujol)<br /> <br /> ==IGT==<br /> *[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) <br /> *[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *Arithmetic <br /> **[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *Denoising<br /> **[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] <br /> **[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Surface Models==<br /> *[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Converters==<br /> *[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<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 /> [[image:UnderConstruction.png|tumb|10px]]<br /> <br /> ==Endoscopy==<br /> *[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br /> <br /> ==[[image:UnderConstruction.png|tumb|10px]] Work in Progress [[image:UnderConstruction.png|tumb|10px]]==<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) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br /> *[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]<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) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> *Registration<br /> **[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> **[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] (Casey Goodlett)[[image:UnderConstruction.png|tumb|10px]]<br /> &lt;!--<br /> **[[Documentation/{{documentation/version}}/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]<br /> --&gt;<br /> *Segmentation<br /> **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/KSliceInteractiveSegmenter&diff=31589 2013-05-12T19:56:11Z

<p>Ikolesov: moved Documentation/4.2/Modules/KSliceInteractiveSegmentor to Documentation/Nightly/Modules/KSliceInteractiveSegmentor:&amp;#32;The extension will be added to the trunk, not to 4.2 stable.</p> <hr /> <div>&lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-header}}<br /> &lt;!-- ---------------------------- --&gt;<br /> <br /> <br /> <br /> <br /> <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 /> <br /> This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].&lt;br&gt;<br /> <br /> Author: Ivan Kolesov, Georgia Institute of Technology&lt;br&gt;<br /> Author: Peter Karasev, Georgia Institute of Technology&lt;br&gt;<br /> Author: Patricio Vela, Georgia Institute of Technology&lt;br&gt;<br /> Author: Allen Tannenbaum, University of Alabama Birmingham&lt;br&gt;<br /> Contributor1: Steve Pieper, Isomics, Inc.&lt;br&gt;<br /> &lt;!--Contributor2: FIRSTNAME LASTNAME, AFFILIATION&lt;br&gt; --&gt;<br /> &lt;!--Contact: FIRSTNAME LASTNAME, &lt;email&gt;john@doe.org&lt;/email&gt;&lt;br&gt; --&gt;<br /> <br /> {{documentation/{{documentation/version}}/module-introduction-row}}<br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br /> |[[File:GeorgiaTech_Logo.svg]]<br /> |{{collaborator|logo|spl}}|{{collaborator|longname|spl}} &lt;-Replace this logo with yours<br /> }} --&gt;<br /> <br /> <br /> {{documentation/{{documentation/version}}/module-introduction-end}}<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Module Description}}<br /> <br /> This is the KSlice interactive segmentation method. It uses a data-driven automatic algorithm to process the majority of the volume. As the automatic segmentation runs and displays the current state, a human user can influence the algorithm’s behavior to more closely align with an expected result.<br /> In the end, the user has created an excellent segmentation result with a minimal amount of time and effort. Please see the references below for more details.<br /> <br /> &lt;!--Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br /> If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:&lt;pre&gt;{{documentation/{{documentation/version}}/module-description}}<br /> {{documentation/{{documentation/version}}/module-description}} --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Use Cases}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Tutorials}}<br /> <br /> Step 1.) Add data volume to segment<br /> <br /> [[File:LoadData.png|500px]]<br /> <br /> <br /> Step 2.) Go to the “Editor” module, select the volume loaded in Step 1 as the “Master Volume” in the “Create and Select Label Maps” drop-down menu<br /> <br /> [[File:StartEditor.png|500px]]<br /> <br /> <br /> Step 3.) Select the “KSlice” effect in the “Edit Selected Label Map” drop-down menu<br /> <br /> [[File:KSliceEffect.png|50px]]<br /> <br /> <br /> Step 4.) Set the “Radius” parameter and press the “Start Interactive Segmentor” button ( KSlice is now running in the background until the “Stop Interactive Segmentor” button is pressed)<br /> <br /> [[File:StartBot.png|500px]]<br /> <br /> <br /> Step 5.) Turn “On” all three slice views in the 3D Plane<br /> <br /> [[File:TurnOnSlices3D.png|500px]]<br /> <br /> <br /> Step 5.) Select the “PaintEffect” tool <br /> (green circle, inside the esophagus in this example)<br /> <br /> [[File:Paint.png|50px]]<br /> <br /> and initialize KSlice by drawing inside the structure of interest<br /> <br /> [[File:KSliceInit.png|500px]]<br /> <br /> Step 6.) Hover the mouse over a slice view (we focus on the “Red” slice first, here) and press the “Q” key to evolve a 2D active contour in this plane<br /> <br /> [[File:Segment2D.png|500px]]<br /> <br /> <br /> Step 7.) Press the “C” key to copy the current segmentation in this 2D plane, then press the left/right arrow on the keyboard to move on to an adjacent slice, press the “V” key to paste the label, thereby initializing the current slice<br /> <br /> [[File:CopyPasteSlice.png|500px]]<br /> <br /> <br /> Step 8.) Evolve the 2D contour on this slice by pressing “Q” <br /> <br /> [[File:Segment2DAfterPaste.png|500px]]<br /> <br /> <br /> Step 9.) Hover mouse over the yellow, then green slices and repeat (as many times as desired) Steps 6-8<br /> <br /> [[File:SegmentAllSlices.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> == As necessary, take steps at any time in the process ==<br /> <br /> Step 10.)(Used in any order) Press the “A” key to change drawing modes (between Draw/Delete label). Thus, if the user's expert knowledge of anatomy does not agree with the current segmentation results, he adds negative input by erasing a label. By deleting in the same area multiple times, the user input is accumulated and this guiding signal forces the changes to become persistent<br /> <br /> [[File:DeleteLabel.png|500px]]<br /> <br /> <br /> Step 11.)(Used in any order) Alternatively, a user can press “A” again to return to drawing. If a contour is not reaching an area that is, in fact, part of the structure of interest, the user can add positive input by painting this area<br /> <br /> [[File:DrawLabel.png|500px]]<br /> <br /> <br /> Step 12.)(Used in any order) Evolve the contour with the changed user input, and new initialization<br /> <br /> [[File:EvolveAfterUserInput.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> <br /> == Optional Visualization ==<br /> <br /> Step 13.) (Optional) Turn on “Volume Rendering” of the label image in 3D (notice the parameters set for faster interaction). This will be updated during the evolution<br /> <br /> [[File:VolumeRederingOn.png|500px]]<br /> <br /> <br /> ---- &lt;!-- Horizontal rule --&gt;<br /> <br /> Step 14.) Evolution in 3D is done by pressing the “W” key<br /> <br /> [[File:Result3DSegmentation.png|500px]]<br /> <br /> Step 15.) Once satisfies with the segmentation, stop KSlice by clicking &quot;Stop Interactive Segmentor&quot;<br /> <br /> [[File:StopKSlice.png|500px]]<br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Panels and their use}}<br /> There is one parameter to set: the radius that sets the band around the current initialisation in which image data is considered. A large radius means data from far lying regions influences the segmentation (this increases the computational complexity). A small radius ensures that only nearby pixels influence the contour (but set too small will require a better contour initialisation from the user)<br /> <br /> <br /> <br /> <br /> &lt;!--{{documentation/{{documentation/version}}/module-parametersdescription}}--&gt;<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> &lt;!-- {{documentation/{{documentation/version}}/module-section|Similar Modules}}<br /> N/A --&gt;<br /> <br /> <br /> <br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|References}}<br /> *Kolesov, I., Karasev, P., Muller, G., Chudy, K., Xerogeanes, J., and Tannenbaum, A., “Human supervisory control framework for interactive medical image segmentation,” in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) Computational Biomechanics for Medicine Workshop, Proceeding of the, 2011.<br /> <br /> *Karasev, P., Kolesov, I., Chudy, K., Muller, G., Xerogeanes, J., and Tannenbaum, A., “Interactive mri segmentation with controlled active vision,” in IEEE Conference on Decision and Control, Proceedings of the, IEEE, Dec. 2011.<br /> <br /> *Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., and Tannenbaum, A.. “Interactive Medical Image Segmentation using PDE Control Of Active Contours”. In: Medical Imaging, IEEE Transactions on (In Submission) (2013)<br /> <br /> *Xerogeanes, J., Mitchell, P. , Karasev, P., Kolesov, I. and Romine, S. . “An Anatomic and Morphologic Evaluation of the Quadriceps Tendon Using 3D MRI Reconstruction: Applications for ACL Autograft Choice and Procurement”. In: Journal of Bone and Joint Surgery (In Submission) (2013)<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-section|Information for Developers}}<br /> {{documentation/{{documentation/version}}/module-developerinfo}}<br /> <br /> <br /> &lt;!-- ---------------------------- --&gt;<br /> {{documentation/{{documentation/version}}/module-footer}}<br /> &lt;!-- ---------------------------- --&gt;</div>

Ikolesov https://www.slicer.org/w/index.php?title=Documentation/4.2/Modules/KSliceInteractiveSegmentor&diff=31590 2013-05-12T19:56:11Z

<p>Ikolesov: moved Documentation/4.2/Modules/KSliceInteractiveSegmentor to Documentation/Nightly/Modules/KSliceInteractiveSegmentor:&amp;#32;The extension will be added to the trunk, not to 4.2 stable.</p> <hr /> <div>#REDIRECT [[Documentation/Nightly/Modules/KSliceInteractiveSegmentor]]</div>

Ikolesov