Difference between revisions of "Documentation/3.6"

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This is work in progress
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<noinclude>{{documentation/versioncheck}}</noinclude>
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[[image:Slicer3-6Announcement-v2.png| right |3.6 Icon]]
  
=Main GUI=
+
{{documentation/versionlist}}
  
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]]
+
=Introduction=
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]]
 
*[[Modules:DataModule-3.6| Loading Scenes and Individual Datasets through the Data Module]]
 
*[[Modules:Loading-Data-3.6| Data Loading Details]]
 
*[[Modules:Saving-Documentation-3.6| Saving Scenes and Data]]
 
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]]
 
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]]
 
  
=Modules=
+
3D Slicer is a flexible platform that can be easily extended to enable development of both interactive and batch processing tools for a variety of applications. 
*Please copy the template linked below, paste it into your page and customize it with your module's information.
+
[[Slicer3:Module_Documentation-3.5_Template|Slicer3:Module_Documentation-3.5_Template]]  '''Not yet 3.6'''
+
3D Slicer provides image registration, processing of DTI (diffusion tractography), an interface to external devices for image guidance support, and GPU-enabled volume rendering, among other capabilities. 3D Slicer has a modular organization that allows the easy addition of new functionality and provides a number of generic features not available in competing tools. Finally, 3D Slicer is distributed under a non-restrictive BSD license.
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
 
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]
 
  
Please adhere to the naming scheme for the module documentation:
+
The interactive visualization capabilities of 3D Slicer include the ability to display arbitrarily oriented image slices, build surface models from image labels, and high performance volume rendering. 3D Slicer also supports a rich set of annotation features (fiducials and measurement widgets, customized colormaps). To the best of our knowledge, no individual segmentation tool provides such powerful visualization capabilities for the user as 3D Slicer. (These paragraphs were provided by A. Fedorov and C. Lisle)
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)
 
  
=Requirements for Modules=
+
The 3.6 release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Announcements:Slicer3.6 |3.6 Announcement page]] for a list of those changes. The community contributing to Slicer 3.6 is [[Announcments-3.6-Team|acknowledged here]].
{| border="00" cellpadding="5" cellspacing="0"
 
|-
 
| rowspan="2"|
 
* The module is '''feature complete''', it does everything that it advertises it can do
 
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
 
* Module has '''documentation''' on the [[Documentation-3.5#Modules|Slicer wiki]]. Please use the template provided [[Documentation-3.5#Modules|'''here''']] to structure your page. Please keep in mind that our users are not computer scientists with a background in computer vision.
 
*Please add a pointer to the documentation on the Slicer wiki to the the '''Help''' tab of the module. See the '''Editor module''' in Slicer for an example.
 
* The contributor (and their manager/advisor), the lab (with labs/institution logo) and the funding source (with grant number, logo optional) are listed in the '''Acknowledegment''' tab of the module. Please see the '''Models module''' for an example. The people listed in the acknowledgement will be the primary people for support and maintenance relative of the module. [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|See here for more information.]]
 
** '''Style Guide:''' All acknowledgment icons should be 100x100 pixels, preferably in png format.
 
** '''Accessing logos:''' Icons for BIRN, NAC, NA-MIC and IGT are included in Slicer3/Base/GUI//vtkSlicerBaseAcknowledgementLogoIcons.cxx/h and resources for them are in Slicer3/Base/GUI/Resources/vtkSlicerBaseAcknowledgementLogos_ImageData.h. The API for vtkSlicerModuleGUI provides access to these icons.
 
** '''Adding logos:''' Please add additional image resources and logo icons to these files as required in order to promote shared use (and to prevent duplication in the code.)
 
* Many modules are better suited to be [[Documentation-3.4#Extensions_for_Downloading|downloadable extensions]].  The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
 
* Follow [[Documentation-3.5-Rons-Rules|"Ron's rules for tools"]]
 
| style="background: #e5e5e5" align="center"| Examples for the Help and
 
Acknowledgment Panels
 
|-
 
| style="background: #ebeced"|[[Image:SlicerHelpExample.png|center|200px]][[Image:SlicerAcknowledgementExample.png|center|200px]]
 
|}
 
  
=List of Modules new to 3.6=
+
*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.
 +
*For information on how to obtain Slicer 3.6 please go to the [http://www.slicer.org/pages/Special:SlicerDownloads Download Pages].
 +
*For sample data see [[SampleData|here]]
 +
*For documentation on other versions of Slicer see [[Documentation|here]]
 +
*For a [[Slicer-3-6-FAQ|FAQ]] see here
 +
*[[Slicer3:Build_Instructions|Slicer version 3 build instructions]] for developers
 +
*<big>For an overview on how to load your data, see [[Slicer-3.6-Load-Overview|here]]</big>
  
=List of pre-existing Modules=
+
=Main GUI=
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume)  '''Not yet 3.6'''
 
* [[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)  '''Not yet 3.6'''
 
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda)  '''Not yet 3.6'''
 
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda)  '''Not yet 3.6'''
 
* [[Modules:FastMarchingSegmentation-Documentation-3.5|Fast Marching segmentation]] (Andriy Fedorov)  '''Not yet 3.6'''
 
* [[Modules:GyriContourSegmentation-Documentation-3.5|Gyri Contour Segmentation]] (Peter Karasev)  '''Not yet 3.6'''
 
* [[Modules:ExtractSubvolumeROI-Documentation-3.5|Subvolume extraction with ROI widget]] (Andriy Fedorov)  '''Not yet 3.6'''
 
* [[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary)  '''Not yet 3.6'''
 
* [[Modules:Measurements-Documentation-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin)  '''Not yet 3.6'''
 
* [[Modules:RegisterImagesMultiRes-Documentation-3.5 | Affine registration ]] (Casey Goodlett)  '''Not yet 3.6'''
 
* [[Modules:CollectFiducials-Documentation-3.5 | Collect Patient Fiducials ]] (Andrew Wiles)  '''Not yet 3.6'''
 
  
===Core===
+
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)  
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''
+
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)  
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''
+
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.)   (Wendy Plesniak)
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)  '''Not yet 3.6'''
+
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.)  (Wendy Plesniak)
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''
+
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich) '''Not yet 3.6'''
+
*[[Modules:StereoViewing-3.6 | Setting up and using stereoscopic viewing ]] (Curt Lisle, Wendy Plesniak)
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]]  (Nicole Aucoin)  '''Not yet 3.6'''
+
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich'''Not yet 3.6'''
 
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''
 
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin) '''Not yet 3.6'''
 
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''
 
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich)  '''Not yet 3.6'''
 
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''
 
  
==Specialized Modules==
+
=Modules=
  
Please adhere to the naming scheme for the module documentation:
+
==Core==
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)
+
*[[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
 +
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)
 +
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)
 +
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
 +
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
 +
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
 +
*[[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper) 
 +
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)
 +
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]]  (Nicole Aucoin)
 +
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
 +
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
 +
*[[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)
 +
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
  
===Wizards===
+
==Wizards==
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov) '''Not yet 3.6'''
+
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta)  '''Not yet 3.6'''
+
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)
===Informatics Modules===
 
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak)  '''Not yet 3.6'''
 
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin)  '''Not yet 3.6'''
 
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)  '''Not yet 3.6'''
 
===Registration===
 
*[[Slicer3:Registration|Overview of all Registration Modules ]]
 
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward)  '''Not yet 3.6'''
 
**[[Modules:RegisterImagesMultires-Documentation-3.6|Register Images Multires]] (Casey Goodlett, Stephen Aylward)  '''Not yet 3.6'''
 
**[[Modules:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett)  '''Not yet 3.6'''
 
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich)  '''Not yet 3.6'''
 
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)  '''Not yet 3.6'''
 
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]]  (Daniel Blezek)  '''Not yet 3.6'''
 
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen) '''Not yet 3.6'''
 
**[[Modules:DemonsRegistration-Documentation-3.6|Demons Registration]] (Tom Vercauteren)  '''Not yet 3.6'''
 
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin)  '''Not yet 3.6'''
 
  
===Segmentation===
+
==Informatics Modules==
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)  '''Not yet 3.6'''
+
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)   
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder)  '''Not yet 3.6'''
+
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder)  '''Not yet 3.6'''
 
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder'''Not yet 3.6'''
 
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)  '''Not yet 3.6'''
 
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''
 
  
===Statistics===
+
==Registration==
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper'''Not yet 3.6'''
+
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.
 +
*[http://www.slicer.org/wiki/Slicer-3-6-FAQ '''Registration FAQ''']
 +
*Fast Registration
 +
**[[Modules:Transforms-Documentation-3.6|Transforms]]:  manual & interactive rigid registration , (Alex Yarmarkovich)
 +
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]:  automated fast affine registration , (Jim Miller) 
 +
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]:  automated fast rigid (6 DOF) registration , (Jim Miller) 
 +
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen) 
 +
*Robust Registration
 +
**[[Modules:RegisterImages-Documentation-3.6|Expert Automated Registration]]:  automated registration (rigid to affine to nonrigid) with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
 +
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content ,  (Casey Goodlett)
 +
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).
 +
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).
 +
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).
 +
*Brain Only Registration
 +
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along the AC-PC line (Nicole Aucoin)
 +
*Non-Raster-Image Data Registration
 +
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity(Casey Goodlett)
 +
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)
 +
* [[Modules:AtlasCreator|Atlas Creator]]: create a statistical atlas (Daniel Haehn, Kilian Pohl)
  
===Diffusion===
+
==Segmentation==
====DWI====
+
*[[Modules:SegmentationOverview3.6|Overview]]
*Estimation
+
**[[Modules:EMSegmenter-3.6|EM Segmenter]] (Kilian Pohl)   
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar'''Not yet 3.6'''
+
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching Segmentation]] (Andriy Fedorov)
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''
+
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
*Filter
+
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)   
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
+
**[[Modules:RobustStatisticsSeg-Documentation-3.6|Robust Statistics Segmentation]] Yi Gao (yigao@gatech.edu).
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer'''Not yet 3.6'''
+
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
+
**[[Modules:GrowCutSegmentation-Documentation-3.6|Grow Cut Segmentation]] (Harini Veeraraghavan)
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal) '''Not yet 3.6'''
 
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''
 
  
====DTI====
+
==Quantification==
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin) '''Not yet 3.6'''
+
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''
+
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)
*Analysis
 
  
===Tractography===
+
==Diffusion MRI==
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)  '''Not yet 3.6'''
+
* [[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion MRI Welcome Module]]
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) '''Not yet 3.6'''
+
* DWI Denoising
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich) '''Not yet 3.6'''
+
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) 
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal) '''Not yet 3.6'''
+
**[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer, C-F Westin) 
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell) '''Not yet 3.6'''
+
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]]  (Antonio Tristán Vega, Santiago Aja-Fernandez) 
 +
* Diffusion Tensor Utilities
 +
**[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar) 
 +
**[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)   
 +
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
 +
* Tractography
 +
**[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar) 
 +
**[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmarkovich, Steve Pieper)  
 +
**[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmarkovich)  
 +
**[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Ryan Eckbo)  
 +
**[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)
 +
* Pipeline
 +
**[[GTRACT_V4 | GTRACT CLI tools]] (Vincent Magnotta)
  
===IGT===
+
==IGT==
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda)   '''Not yet 3.6'''
+
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''
+
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''
+
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
===Filtering===
+
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''
+
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''
+
 
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich)  '''Not yet 3.6'''
+
==Time Series==
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''
+
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin) '''Not yet 3.6'''
+
 
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin) '''Not yet 3.6'''
+
==Filtering==
 +
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov)
 +
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
 +
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
 +
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
 +
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)   
 +
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
 +
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)  
 +
*[[Registration:Resampling|'''Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)
 +
**[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
 +
**[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
 +
**[[Modules:ModelTransform-Documentation-3.6|Model Transform]]: "Resample triangulated surface models" (Alex Yarmarkovich)
 
*Arithmetic
 
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''
+
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)  
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen'''Not yet 3.6'''
+
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)   
** [[Modules:CastImage-Documentation-3.4|Cast Image]] (Nicole Aucoin) '''Not yet 3.6'''
+
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)  
** [[Modules:MaskImage-Documentation-3.4|Mask Image]] (Steve Pieper) '''Not yet 3.6'''
+
** [[Modules:MaskImage-Documentation-3.6|Mask Image]] (Nicole Aucoin) Can be used to apply a mask such as a brain mask to a grey scale image
 +
**[[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)
 
*Denoising
 
*Denoising
**[[Modules:GradientAnisotropicFilter-Documentation-3.4| Gradient Anisotropic Filter]]  (Bill Lorensen checked this in) '''Not yet 3.6'''
+
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]]  (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) '''Not yet 3.6'''
+
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward)   '''Not yet 3.6'''
+
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Bill Lorensen'''Not yet 3.6'''
+
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao)   
 
*Morphology
 
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Bill Lorensen'''Not yet 3.6'''
+
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)   
**[[Modules:GrayscaleFillHole-Documentation-3.4|Grayscale Fill Hole]] (Bill Lorensen) '''Not yet 3.6'''
+
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
**[[Modules:GrayscaleGrindPeak-Documentation-3.4|Grayscale Grind Peak]] (Bill Lorensen)  '''Not yet 3.6'''
+
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)
 +
 
 +
==Surface Models==
 +
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)
 +
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
 +
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev) 
 +
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Surface Connectivity]] (Luca Antiga, Daniel Blezek)
 +
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Surface Toolbox]] (Luca Antiga, Daniel Blezek)
 +
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich) 
 +
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
 +
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
 +
*[[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak)
 +
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)
 +
 
 +
==Converters==
 +
*[[Modules:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
 +
*[[Modules:CreateaDicomSeries-Documentation-3.6|Create a Dicom Series]]  (Xiaodong Tao) 
 +
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
 +
*[[Modules:OrientImages-Documentation-3.6|Orient Images]] (Xiaodong Tao) 
 +
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Explode Volume Transform]] (Luca Antiga, Daniel Blezek)
  
===Surface Models===
+
==Endoscopy==
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin) '''Not yet 3.6'''
+
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)
*Grayscale Model Maker (Bill Lorensen)  '''Not yet 3.6'''
 
  
*Freesurfer Surface Section Extraction (Katharina Quintus)
+
==Slicer Extensions==
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)  '''Not yet 3.6'''
 
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)  '''Not yet 3.6'''
 
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)  '''Not yet 3.6'''
 
*[[Modules:ClipModel-Documentation-3.4| Clip Model]] (Alex Yarmarkovich)  '''Not yet 3.6'''
 
*[[Slicer3:Model_Into_Label_Volume_Documentation-3.4| Model into Label Volume]] (Nicole Aucoin)  '''Not yet 3.6'''
 
  
===Batch processing===
 
*[[Modules:EMSegmentBatch-Documentation-3.4|EM Segmenter batch]] (Julien Jomier, Brad Davis)  '''Not yet 3.6'''
 
*[[Modules:GaussianBlurBatch-Documentation-3.4|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)  '''Not yet 3.6'''
 
*[[Modules:RegisterImagesBatch-Documentation-3.4|Register Images batch]] (Julien Finet, Stephen Aylward)  '''Not yet 3.6'''
 
*[[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Volume batch]] (Julien Finet)  '''Not yet 3.6'''
 
  
===Converters===
+
'''Introduction'''
*[[Modules:CreateaDicomSeries-Documentation-3.4|Create a Dicom Series]] (Bill Lorensen)  '''Not yet 3.6'''
 
*[[Modules:DicomToNRRD-3.4|Dicom to NRRD]] (Xiaodong Tao)  '''Not yet 3.6'''
 
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Bill Lorensen)  '''Not yet 3.6'''
 
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.4| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)  '''Not yet 3.6'''
 
*[[Modules:ExtractSubvolume-Documentation-3.4| Extract Subvolume]] (Steve Pieper)  '''Not yet 3.6'''
 
  
=Slicer Extensions=
+
* Slicer Extensions are the "on-ramp" to the Slicer "highway". They provide are a mechanism for anybody, including third parties, to provide modules which extend the functionality of 3d Slicer.
 +
*'''While the Slicer license is suggested, it is not required for extensions. Please review the documentation of the extension carefully.'''
 +
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions.
 +
* The version that is available through the extension manager is chosen by the developer of that extension
 +
* Not all extensions are available on all platforms. See here for the [[Documentation-3.6:ExtensionStatus|extension status]].
 +
* In case of problems with extensions, please talk directly to the developers of the extensions.
 +
* Information for developers can be found [[Slicer3:Extensions|here]].
  
==Extensions for Downloading==
 
===Introduction===
 
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
 
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
 
* Some of the extensions do not use the Slicer license. Please review carefully.
 
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
 
* The version that is available through the extension manager is chosen by the developer of that extension 
 
  
We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
+
'''Available Extensions'''
Click [http://www.nitrc.org/search/?type_of_search=soft&words=slicer3&Search.x=0&Search.y=0&Search=Search  here] to see a listing of Slicer 3 extensions on NITRC.
+
 
 +
* Import/Export
 +
** [[Modules:PlastimatchDICOMRT|Plastimatch > DICOM-RT Import]] Greg Sharp (gcsharp@partners.org).
 +
* Segmentation
 +
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
 +
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .
 +
** [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
 +
** [[Modules:SkullStripperModule|SkullStripperModule]] '''(in progress)''' Xiaodong Tao (taox AT research.ge.com).
 +
** [[Modules:SPECTRE-Documentation-3.6|SPECTRE]] '''(in progress)''' Nicole Aucoin (nicole@bwh.harvard.edu), Min Chen (mchen55@jhu.edu)
 +
* Registration
 +
**Robust
 +
*** [[Modules:CMTK|CMTK]] Torsten Rohlfing (torsten@synapse.sri.com) (a.k.a. Computational Morphometry Toolkit) 
 +
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
 +
** [[Modules:Plastimatch|Plastimatch > B-spline deformable registration]] Greg Sharp (gcsharp@partners.org).
 +
** [[Modules:PlastimatchLANDWARP|Plastimatch > Landmark-based registration]] Nadya Shusharina (nshusharina@partners.org).  
 +
** [[Modules:PlastimatchXFORMWARP|Plastimatch > Warping with transform]] Nadya Shusharina, Greg Sharp (gcsharp@partners.org)
 +
* Wizards
 +
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
 +
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mark-scully[at]uiowa[dot]edu) (a.k.a. 3DSlicerLupusLesionModule) .
 +
* Tractography
 +
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).
 +
* DWI
 +
** [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
 +
* Time Series
 +
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
 +
* Quantification
 +
** [[Modules:LabelDiameterEstimation-Documentation-3.6|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
 +
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)
 +
 
 +
:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins
 +
 
 +
:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models
 +
 
 +
:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface
 +
 
 +
:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution
 +
 
 +
:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures
 +
 
 +
'''Installation Instructions'''
 +
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
 +
[[image:Slicertoolbar.png|Extensions Wizard]]
 +
 
  
 
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
 
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|Extension manager dialog box]]
Line 201: Line 240:
  
  
*Extensions are compiled as part of the nightly build. In order to have your extension compiled nightly and made available to end users, please contact the Slicer team. For explanations for developers see [[Slicer3:Extensions| here]]
 
  
'''Installation'''
+
'''Info for Developers'''
*Click on the icon to start the extensions wizard
+
For explanations for developers see [[Slicer3:Extensions| here]]
[[image:ExtensionsWizard.png|Extensions Wizard]]
+
 
 +
=Other information=
  
===Listing of available plug-ins===
+
'''Developer Tools'''
* VMTK (Daniel Haehn)
+
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
**You need to install the [[Modules:VMTKSlicerModule|VmtkSlicerModule]] to run any of the other three.  '''Not yet 3.6'''
+
*Note: most developer tools are not documented for end users, but contain comments in the source code
**[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] - providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface  '''Not yet 3.6'''
+
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
**[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] - providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms  '''Not yet 3.6'''
+
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
**[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] - providing vessel enhancement filters to highlight vasculature or tubular structures  '''Not yet 3.6'''
+
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)
  
* [[Modules:EMDTIClustering-Documentation-3.5|EM DTI Clustering]] (Mahnaz Maddah)  '''Not yet 3.6'''
 
  
* [[Modules:LabelDiameterEstimation-Documentation-3.5|Label Diameter Estimation]] (Andriy Fedorov)  '''Not yet 3.6'''
+
'''Non-SPL Supported Compatibility Packages'''
 +
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''
  
* [[Modules:ABC-Documentation-3.5|ABC]] (Marcel Prastawa)  '''Not yet 3.6'''
 
* [[Modules:HAMMER]] (GuorongWu, XiaodongTao, JimMiller, DinggangShen)  '''Not yet 3.6'''
 
  
===Extensions Contact List===
+
'''QA Table'''
This is a first pass list of extension authors; more to come!
 
  
{|
+
[[Slicer-3.6-QA|Slicer 3.6 QA table]]
|ABC                    ||      Marcel Prastawa || prastawa@sci.utah.edu
 
|-
 
|EMFiberClusteringModule|| Mahnaz Maddah  || maddah @nospam@ ge.com
 
|-
 
|BRAINSROIAuto || Greg Harris || gregory-harris @nospam@ uiowa.edu
 
|-
 
|Bubble Maker || Carlos Mendoza || carlos.sanchez.medoza @nospam@ gmail.com
 
|-
 
|Hammer Registration || Dinggang Shen || dgshen @nospam@ med.unc.edu
 
|-
 
|Lupus Lesion || Mark Scully    || mscully @nospam@ mrn.org
 
|-
 
|VmtkSlicerModule ||      Daniel Haehn    || haehn @nospam@ bwh.harvard.edu
 
|-
 
|Vmtkin3DSlicer ||      Daniel Haehn    || haehn @nospam@ bwh.harvard.edu
 
|-
 
|BRAINSFit || Eun Young Kim  || eunyoung-kim @nospam@ uiowa.edu
 
|-
 
|ARCTIC || Cedric Mathieu  || ced.mathieu @nospam@ gmail.com
 
|}
 

Latest revision as of 17:05, 21 November 2019

Home < Documentation < 3.6


For the latest Slicer documentation, visit the read-the-docs.


3.6 Icon

Nightly 4.10 4.8 4.6 4.5 4.4 4.3 4.2 4.1 4.0 3.6 3.5 3.4 3.2 ALL VERSIONS

Introduction

3D Slicer is a flexible platform that can be easily extended to enable development of both interactive and batch processing tools for a variety of applications.

3D Slicer provides image registration, processing of DTI (diffusion tractography), an interface to external devices for image guidance support, and GPU-enabled volume rendering, among other capabilities. 3D Slicer has a modular organization that allows the easy addition of new functionality and provides a number of generic features not available in competing tools. Finally, 3D Slicer is distributed under a non-restrictive BSD license.

The interactive visualization capabilities of 3D Slicer include the ability to display arbitrarily oriented image slices, build surface models from image labels, and high performance volume rendering. 3D Slicer also supports a rich set of annotation features (fiducials and measurement widgets, customized colormaps). To the best of our knowledge, no individual segmentation tool provides such powerful visualization capabilities for the user as 3D Slicer. (These paragraphs were provided by A. Fedorov and C. Lisle)

The 3.6 release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the 3.6 Announcement page for a list of those changes. The community contributing to Slicer 3.6 is acknowledged here.

Main GUI

Modules

Core

Wizards

Informatics Modules

Registration

Segmentation

Quantification

Diffusion MRI

IGT

Time Series

Filtering

Surface Models

Converters

Endoscopy

Slicer Extensions

Introduction

  • Slicer Extensions are the "on-ramp" to the Slicer "highway". They provide are a mechanism for anybody, including third parties, to provide modules which extend the functionality of 3d Slicer.
  • While the Slicer license is suggested, it is not required for extensions. Please review the documentation of the extension carefully.
  • For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions.
  • The version that is available through the extension manager is chosen by the developer of that extension
  • Not all extensions are available on all platforms. See here for the extension status.
  • In case of problems with extensions, please talk directly to the developers of the extensions.
  • Information for developers can be found here.


Available Extensions

  • VMTKLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution

Installation Instructions

  • Click on the cogwheel icon to start the extensions wizard (highlighted in red)

Extensions Wizard


Extension manager dialog box

To add extension modules to an installed binary of slicer:

  • Use the View->Extension Manager menu option
  • The dialog will be initialized with the URL to the extensions that have been compiled to match your binary of slicer.
    • Note installing extensions from a different repository URL is likely to be unstable due to platform and software version differences.
    • You can select a local install directory for your downloaded extensions (be sure to choose a directory with enough free space).
  • Select the extensions you wish to install and click to download them. Installed extensions will be available when you restart slicer.
  • To turn modules on or off, you can use the Module Settings page of the View->Application Settings dialog.


Info for Developers

For explanations for developers see  here

Other information

Developer Tools


Non-SPL Supported Compatibility Packages


QA Table

Slicer 3.6 QA table