Difference between revisions of "Documentation/4.1"
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==Registration== | ==Registration== | ||
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]] |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]] |
*Specialized | *Specialized | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin) |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/FiducialRegistration|Fiducial Registration]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]] |
**Vector Demon Registration (Hans Johnson) | **Vector Demon Registration (Hans Johnson) | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/Reformat|Reformat]] (Michael Jeulin-Lagarrigue) |
==Segmentation== | ==Segmentation== | ||
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/SimpleRegionGrowingSegmentation|Simple Region Growing Segmentation]] (Jim Miller, Harini Veeraraghavan) |
*Specialized | *Specialized | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl) |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/RobustStatisticsSegmenter|Robust Statistics Segmenter]] (Yi Gao) |
==Quantification== | ==Quantification== | ||
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper) | *[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper) | ||
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/LabelStatistics|Label Statistics]] (Steve Pieper) |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/PETStandardUptakeValueComputation|PET Standard Uptake Value Computation]] (Nicole Aucoin) |
* Change quantification | * Change quantification | ||
| − | ** [[Documentation/ | + | ** [[Documentation/{{documentation/version}}/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov) |
==Diffusion== | ==Diffusion== | ||
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]] | *DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]] | ||
*Denoising | *Denoising | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/DWIJointRicianLMMSEFilter|DWI Joint Rician LMMSE Image Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/DWIRicianLMMSEFilter|DWI Rician LMMSE Filter]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]] |
*Tractography | *Tractography | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/TractographyLabelMapSeeding|Tractography Label Map Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]] |
*Utilities | *Utilities | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/DWIToDTIEstimation|DWI To DTI Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/DiffusionTensorScalarMeasurements|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/DiffusionWeightedVolumeMasking|Diffusion Weighted Volume Masking]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/ResampleDTIVolume|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]] |
==IGT== | ==IGT== | ||
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/OpenIGTLinkIF| OpenIGTLink IF]] (Junichi Tokuda) [[image:UnderConstruction.png|tumb|10px]] |
==Filtering== | ==Filtering== | ||
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov) |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/CheckerBoardFilter|CheckerBoard Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]] |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/ThresholdScalarVolume|Threshold Scalar Volume]] (Nicole Aucoin) |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
*Arithmetic | *Arithmetic | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/AddScalarVolumes|Add Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/CastScalarVolume| Cast Scalar Volume]] (Nicole Aucoin) |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/MaskScalarVolume| Mask Scalar Volume]] (Nicole Aucoin) |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/MultiplyScalarVolumes| Multiply Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/SubtractScalarVolumes| Subtract Scalar Volumes]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
*Denoising | *Denoising | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/GaussianBlurImageFilter|Gaussian Blur Image Filter]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
*Morphology | *Morphology | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole Image Filter]] (Jim Miller) |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/GrayscaleGrindPeakImageFilter|GGrayscale Grind Peak Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
==Surface Models== | ==Surface Models== | ||
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/LabelMapSmoothing|Label Map Smoothing]] [[image:UnderConstruction.png|tumb|10px]] |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/MergeModels| Merge Models]] (Nicole Aucoin) |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/ModelToLabelMap| Model To LabelMap]] (Nicole Aucoin) |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/ProbeVolumeWithModel| Probe Volume With Model]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]] |
==Converters== | ==Converters== | ||
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/CreateDICOMSeries|Create DICOM Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov) |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/OrientScalarVolume| Orient Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
==Endoscopy== | ==Endoscopy== | ||
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/Endoscopy|Endoscopy]] (Steve Pieper) |
==Developer Tools== | ==Developer Tools== | ||
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]] |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]] |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]] |
| − | *[[Documentation/ | + | *[[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Module Template]] (JC Fillion-Robin) |
*Performance Tests | *Performance Tests | ||
*Tractography | *Tractography | ||
| Line 252: | Line 252: | ||
==Legacy== | ==Legacy== | ||
*Converters | *Converters | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/BSplineToDeformationField|BSpline To Deformation Field]] |
*Diffusion | *Diffusion | ||
**Denoising | **Denoising | ||
| − | ***[[Documentation/ | + | ***[[Documentation/{{documentation/version}}/Modules/DWIUnbiasedNonLocalMeansFilter|DWI Unbiased Non Local Means Filter]] |
*Filtering | *Filtering | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdImageFilter|Otsu Threshold Image Filter]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|Resample Scalar Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
*Registration | *Registration | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/BSplineDeformableRegistration|BSpline Deformable Registration]] [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/ExpertAutomatedRegistration|Expert Automated Registration]] [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]] |
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/MultiResolutionAffineRegistration|MultiResolution Affine Registration]] [[image:UnderConstruction.png|tumb|10px]] |
<!-- | <!-- | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]] |
--> | --> | ||
*Segmentation | *Segmentation | ||
| − | **[[Documentation/ | + | **[[Documentation/{{documentation/version}}/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]] |
=Extensions= | =Extensions= | ||
Revision as of 19:52, 12 April 2012
Home < Documentation < 4.1
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
Table of Content
Slicer Application
Mailing Lists
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Module Categories |
Miscellaneous
Developers Corner
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General Information
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Modules by Category
Core Modules
- Annotations (Nicole Aucoin)
- Colors (Nicole Aucoin)
- Data (Julien Finet)
- DICOM (Steve Pieper)
- Editor (Steve Pieper)
- Models (Nicole Aucoin)
- SceneViews (Nicole Aucoin)
- Transforms (Alex Yarmarkovich)
- View Controllers (Jim Miller)
- Volumes (Steve Pieper)
- Volume Rendering (Julien Finet)
- Welcome to Slicer (Wendy Plesniak)
Wizards
- ChangeTracker (Andrey Fedorov)
Informatics
- Sample Data (Steve Pieper)
Registration
- General Brainsfit Registration (Hans Johnson)
- Resample Image (BRAINS) (Hans Johnson)
- Specialized
- ACPC Transform (Nicole Aucoin)
- Demon Registration (BRAINS) (Hans Johnson)
- Fiducial Registration (Stephen Aylward)
- Vector Demon Registration (Hans Johnson)
- Reformat (Michael Jeulin-Lagarrigue)
Segmentation
- EMSegment Easy (no atlas) (Kilian Pohl)
- EMSegment (with atlas) (Kilian Pohl)
- Simple Region Growing Segmentation (Jim Miller, Harini Veeraraghavan)
- Specialized
- EMSegment Command-line (Kilian Pohl)
- Foreground Masking (BRAINS) (Hans Johnson)
- Mesh Contour Segmentation (Allen Tannenbaum)
- Robust Statistics Segmenter (Yi Gao)
Quantification
- Data Probe (Steve Pieper)
- Label Statistics (Steve Pieper)
- PET Standard Uptake Value Computation (Nicole Aucoin)
- Change quantification
- Intensity Difference Metric (Andrey Fedorov)
Diffusion
- DWI to Full Brain Tractography (Demian Wasserman)
- Denoising
- DWI Joint Rician LMMSE Image Filter (Demian Wasserman)
- DWI Rician LMMSE Filter (Demian Wasserman)
- DWI Joint Rician LMMSE Image Filter (Demian Wasserman)
- Tractography
- Tractography Display (Demian Wasserman)
- Tractography Fiducial Seeding (Demian Wasserman)
- Tractography Label Map Seeding (Demian Wasserman)
- Tractography Display (Demian Wasserman)
- Utilities
- DWI To DTI Estimation (Demian Wasserman)
- Diffusion Tensor Scalar Measurements (Demian Wasserman)
- Diffusion Weighted Volume Masking (Demian Wasserman)
- Resample DTI Volume (Demian Wasserman)
- DWI To DTI Estimation (Demian Wasserman)
IGT
- OpenIGTLink IF (Junichi Tokuda)
Filtering
- N4ITK Bias Field Correction (Andrey Fedorov)
- CheckerBoard Filter (Jim Miller)
- Extract Skeleton (Jim Miller)
- Histogram Matching (Jim Miller)
- Image Label Combine (Alex Yarmarkovich)
- Resample Scalar/Vector/DWI Volume (Francois Budin)
- Threshold Scalar Volume (Nicole Aucoin)
- Voting Binary Hole Filling Image Filter (Jim Miller)
- Arithmetic
- Add Scalar Volumes (Jim Miller)
- Cast Scalar Volume (Nicole Aucoin)
- Mask Scalar Volume (Nicole Aucoin)
- Multiply Scalar Volumes (Jim Miller)
- Subtract Scalar Volumes (Jim Miller)
- Add Scalar Volumes (Jim Miller)
- Denoising
- Gradient Anisotropic Diffusion (Jim Miller)
- Curvature Anisotropic Diffusion (Jim Miller)
- Gaussian Blur Image Filter (Stephen Aylward)
- Median Image Filter (Jim Miller)
- Gradient Anisotropic Diffusion (Jim Miller)
- Morphology
- Grayscale Fill Hole Image Filter (Jim Miller)
- GGrayscale Grind Peak Image Filter (Jim Miller)
Surface Models
- Grayscale Model Maker (Jim Miller)
- Label Map Smoothing
- Merge Models (Nicole Aucoin)
- Model Maker (Nicole Aucoin)
- Model To LabelMap (Nicole Aucoin)
- Probe Volume With Model (Lauren O'Donnell)
Converters
- Create DICOM Series (Jim Miller)
- Crop Volume (Andrey Fedorov)
- Dicom to Nrrd Converter (Jim Miller)
- Orient Scalar Volume (Jim Miller)
Endoscopy
- Endoscopy (Steve Pieper)
Developer Tools
- Cameras (Julien Finet)
- Event Broker (Julien Finet)
- Execution Model Tour (JC Fillion-Robin)
- Module Template (JC Fillion-Robin)
- Performance Tests
- Tractography
Legacy
- Converters
- Diffusion
- Denoising
- Filtering
- MRI Bias Field Correction (Sylvain Jaume)
- Otsu Threshold Image Filter (Bill Lorensen)
- Resample Scalar Volume (Jim Miller)
- MRI Bias Field Correction (Sylvain Jaume)
- Registration
- Segmentation
- Otsu Threshold Segmentation (Bill Lorensen)
- Otsu Threshold Segmentation (Bill Lorensen)
Extensions
Introduction
- Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.
- While the Slicer license is suggested for extensions, it is not required. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.
- 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 extensions, please talk directly to the developers of the extensions.
- Information for developers can be found here. See here for the end-user documentation template.
- In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.
Collections
Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.
| id | Thumbnail | Name | Short Description | Maturity | Slicer License | Search terms | Contact Information |
|---|---|---|---|---|---|---|---|
| 1 | 
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MyCollection | This is a collection of extensions that will do something miraculous with your images | 
|
|
segmentation, level set | my-email at mit.edu |
Table Of Extensions
| id | Thumbnail | Name | Short Description | Maturity | Slicer License | Search terms | Contact Information |
|---|---|---|---|---|---|---|---|
| 1 | 
|
MyExtension | This is an extension that will do something wonderful with your data | 
|
|
filter, anisotropic | my-email at gmail.com |
| 2 |
|
MyExtension | This is an extension that will do something miraculous with your images |
|
|
segmentation, level set | my-email at mit.edu |
Caption for the table of extensions
Distributed under the Slicer License
Distributed under a Non Slicer License
Work in progress (aka mess)
Use with care
Might not work all the time
Might not be available for all platforms
Stable
Full documentation
Works as advertised
Compiles on all supported platforms
Email support works
