Difference between revisions of "Documentation/3.6"

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<noinclude>{{documentation/versioncheck}}</noinclude>
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[[image:Slicer3-6Announcement-v2.png| right |3.6 Icon]]
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{{documentation/versionlist}}
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=Introduction=
 
=Introduction=
  
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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.
 
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.
  
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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 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 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 [[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]].
  
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The 3.6 release contains significant changes both to the organization of the software and the functionality. Please check the [[Announcements:Slicer3.6 |3.6 Announcement page]] for a list of those changes and for [[Announcments-3.6-Team|acknowledgments]] of the contributors.
+
*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.
−
*For information on how to use Slicer 3.6 please go to the tutorial pages.
 
 
*For information on how to obtain Slicer 3.6 please go to the [http://www.slicer.org/pages/Special:SlicerDownloads Download 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>
  
 
=Main GUI=
 
=Main GUI=
  
−
*[[Image:WeakDoc.png]][[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)  
+
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)  
 
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)  
 
*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)  
 
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.)  (Wendy Plesniak)
 
*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.)  (Wendy Plesniak)
 
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.)  (Wendy Plesniak)
 
*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.)  (Wendy Plesniak)
 
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
 
*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
−
*[[Image:WeakDoc.png]][[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] '''in progress''' (Wendy Plesniak)
+
*[[Modules:StereoViewing-3.6 | Setting up and using stereoscopic viewing ]] (Curt Lisle, Wendy Plesniak)
 +
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)
  
 
=Modules=
 
=Modules=
  
 
==Core==
 
==Core==
−
*[[Image:WeakDoc.png]][[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
+
*[[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:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)  
 
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)  
 
*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)  
−
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (CF Westin)
+
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
 
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)  
 
*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)  
−
*[[Image:WeakDoc.png]][[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
+
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
−
*[[Image:MissingOrStaleDoc.png]][[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)   
+
*[[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)   
 
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)  
 
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)  
 
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]]  (Nicole Aucoin)  
 
*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]]  (Nicole Aucoin)  
 
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
 
*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
−
*[[Image:WeakDoc.png]][[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
+
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
−
*[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)  
+
*[[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)  
 
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
 
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
  
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==Registration==
 
==Registration==
 
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.
 
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.
−
*Fast
+
*[http://www.slicer.org/wiki/Slicer-3-6-FAQ '''Registration FAQ''']
−
**[[Image:WeakDoc.png]][[Modules:Transforms-Documentation-3.6|Transforms]]:  manual & interactive rigid registration , (Alex Yarmarkovich)
+
*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: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: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)   
 
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)   
−
*Robust
+
*Robust Registration
−
**[[Modules:RegisterImages-Documentation-3.6|Expert Pipeline Rigid-Affine-Nonrigid Registration]]:  automated registration with extensive parameter options, robust initialization, variable DOF and masking options, (Casey Goodlett)
+
**[[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: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)
−
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).
+
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).
−
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).
+
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).
−
** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).
+
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).
−
 
+
*Brain Only Registration
−
*Brain Only
+
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along the AC-PC line (Nicole Aucoin)
−
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
+
*Non-Raster-Image Data Registration
−
*Non-Raster-Image Data
 
 
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity)  (Casey Goodlett)
 
**[[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: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)
  
 
==Segmentation==
 
==Segmentation==
 
*[[Modules:SegmentationOverview3.6|Overview]]
 
*[[Modules:SegmentationOverview3.6|Overview]]
−
**[[Modules:EMSegmentTemplateBuilder3.6|EM Segment Template Builder 3.6]] (Kilian Pohl) 
+
**[[Modules:EMSegmenter-3.6|EM Segmenter]] (Kilian Pohl)   
−
**[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line]] (Kilian Pohl)   
+
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching Segmentation]] (Andriy Fedorov)
−
**[[Modules:EMSegment-Simple3.6|EM Segment Simple]] (Kilian Pohl)
 
−
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
 
 
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
 
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
−
**[[Image:MissingOrStaleDocLink.png]][[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)   
+
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)   
−
**[[Modules:RobustStatisticsSeg-Documentation-3.6|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu).
+
**[[Modules:RobustStatisticsSeg-Documentation-3.6|Robust Statistics Segmentation]] Yi Gao (yigao@gatech.edu).
−
**[[Image:MissingOrStaleDoc.png]][[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).
+
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).
 +
**[[Modules:GrowCutSegmentation-Documentation-3.6|Grow Cut Segmentation]] (Harini Veeraraghavan)
  
 
==Quantification==
 
==Quantification==
 
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
 
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
−
*[[Image:WeakDoc.png]][[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)
+
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)
  
 
==Diffusion MRI==
 
==Diffusion MRI==
−
*Diffusion MRI
+
* [[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion MRI Welcome Module]]
−
** DWI filtering
+
* DWI Denoising
−
***[[Image:MissingOrStaleDocLink.png]][[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)   
+
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)   
−
***[[Image:MissingOrStaleDocLink.png]][[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)   
+
**[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer, C-F Westin)   
−
***[[Image:MissingOrStaleDocLink.png]][[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]]  (Antonio Tristán Vega, Santiago Aja-Fernandez)   
+
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]]  (Antonio Tristán Vega, Santiago Aja-Fernandez)   
−
** Diffusion tensor utilities
+
* Diffusion Tensor Utilities
−
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)   
+
**[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)   
−
***[[Image:MissingOrStaleDocLink.png]][[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)   
+
**[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)   
−
** Resampling
+
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
−
***[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
+
* Tractography
−
** Tractography
+
**[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)   
−
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)   
+
**[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmarkovich, Steve Pieper)  
−
***[[Image:MissingOrStaleDocLink.png]][[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)  
+
**[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmarkovich)  
−
***[[Image:MissingOrStaleDocLink.png]][[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)  
+
**[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Ryan Eckbo)   
−
***[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Julien de Siebenthal)   
+
**[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)
−
***[[Image:MissingOrStaleDocLink.png]][[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)
+
* Pipeline
 +
**[[GTRACT_V4 | GTRACT CLI tools]] (Vincent Magnotta)
  
 
==IGT==
 
==IGT==
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==Filtering==
 
==Filtering==
−
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov), based on most recent version of ITK
+
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov)
 
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
 
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
 
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
 
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
 
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]]  (Bill Lorensen, Xiaodong Tao)
 
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]]  (Bill Lorensen, Xiaodong Tao)
−
*[[Image:MissingOrStaleDocLink.png]][[Image:WeakDoc.png]][[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)   
+
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)   
−
*[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
 
−
*[[Image:MissingOrStaleDoc.png]][[Modules:ResampleVolumeBatch-Documentation-3.4|Resample Scalar Volume Batch Make]]  (Julien Finet)
 
−
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
 
−
*[[Modules:ModelTransform-Documentation-3.6|Model Transform]] (Alex Yarmarkovich)
 
 
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
 
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
 
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)  
 
*[[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-3.6|Add Images]] (Harini Veeraraghavan)  
 
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)  
Line 125: Line 138:
 
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)  
 
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)  
 
** [[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: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
−
**[[Image:WeakDoc.png]][[Image:MissingOrStaleDocLink.png]][[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)  
+
**[[Modules:MultiplyImages-Documentation-3.6|Multiply Images]] (Harini Veeraraghavan)  
 
*Denoising
 
*Denoising
 
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]]  (Bill Lorensen)
 
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]]  (Bill Lorensen)
Line 139: Line 152:
 
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)  
 
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)  
 
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
 
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
−
*[[Image:MissingOrStaleDocLink.png]][[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)   
+
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)   
−
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceConnectivity-Documentation-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek)
+
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Surface Connectivity]] (Luca Antiga, Daniel Blezek)
−
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)
+
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Surface Toolbox]] (Luca Antiga, Daniel Blezek)  
−
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)  
+
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)   
−
*[[Image:MissingOrStaleDocLink.png]][[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)   
 
 
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
 
*[[Modules:Model_Into_Label_Volume_Documentation-3.6| Model into Label Volume]] (Nicole Aucoin)
 
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
 
*[[Modules:MergeModels-Documentation-3.6| Merge Models]] (Nicole Aucoin)
−
*[[Image:MissingOrStaleDoc.png]][[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak) ('''in progress''')
+
*[[Modules:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak)  
 
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)
 
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)
  
Line 154: Line 166:
 
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
 
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] (Xiaodong Tao)
 
*[[Modules:OrientImages-Documentation-3.6|Orient Images]]  (Xiaodong Tao)   
 
*[[Modules:OrientImages-Documentation-3.6|Orient Images]]  (Xiaodong Tao)   
−
*[[Image:MissingOrStaleDocLink.png]][[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)
+
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Explode Volume Transform]] (Luca Antiga, Daniel Blezek)
  
 
==Endoscopy==
 
==Endoscopy==
Line 160: Line 172:
  
 
==Slicer Extensions==
 
==Slicer Extensions==
 +
  
 
'''Introduction'''
 
'''Introduction'''
−
* 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.
+
* 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.
−
* 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.
+
*'''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
 
* 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]].
 +
  
 
'''Available Extensions'''
 
'''Available Extensions'''
  
 +
* Import/Export
 +
** [[Modules:PlastimatchDICOMRT|Plastimatch > DICOM-RT Import]] Greg Sharp (gcsharp@partners.org).
 
* Segmentation
 
* Segmentation
 
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.  
 
** [[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:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .
−
** [[Image:MissingOrStaleDoc.png]][[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).  
+
** [[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
 
* Registration
 
**Robust
 
**Robust
−
*** [[Image:MissingOrStaleDoc.png]][[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) .
+
*** [[Modules:CMTK|CMTK]] Torsten Rohlfing (torsten@synapse.sri.com) (a.k.a. Computational Morphometry Toolkit) 
−
*** [[Image:MissingOrStaleDoc.png]][[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com).  
 
 
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).  
 
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).  
−
*** [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org).
+
** [[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
 
* Wizards
 
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .  
 
** [[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 (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
+
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mark-scully[at]uiowa[dot]edu) (a.k.a. 3DSlicerLupusLesionModule) .
−
** [[Image:MissingOrStaleDoc.png]][[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com).  
 
 
* Tractography
 
* Tractography
−
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools).
+
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).
 
* DWI
 
* DWI
−
** [[Image:MissingOrStaleDoc.png]][[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
+
** [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
 
* Time Series
 
* 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)
 
** [[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
 
* Quantification
−
** [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .  
+
** [[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)
 
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)
  
Line 220: Line 242:
  
 
'''Info for Developers'''
 
'''Info for Developers'''
−
 
+
  For explanations for developers see [[Slicer3:Extensions| here]]
−
*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.
 
−
*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.
 
−
 
 
−
*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]]
 
−
 
 
−
 
 
−
* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller
 
−
 
 
−
* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper
 
−
 
 
−
* [[Image:MissingOrStaleDoc.png]][[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper
 
−
 
 
−
* [[Image:MissingOrStaleDoc.png]][[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper
 
−
 
 
−
* [[Image:MissingOrStaleDoc.png]][[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper
 
  
 
=Other information=
 
=Other information=
Line 242: Line 249:
 
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
 
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
 
*Note: most developer tools are not documented for end users, but contain comments in the source code
 
*Note: most developer tools are not documented for end users, but contain comments in the source code
−
 
−
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
 
 
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
 
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
 
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
 
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
Line 253: Line 258:
  
  
−
 
+
'''QA Table'''
−
 
 
−
'''QA'''
 
−
Key for flagged modules below:
 
−
 
 
−
[[Image:MissingOrStaleDoc.png]]: No 3.6 Documentation
 
−
 
 
−
[[Image:MissingOrStaleDocLink.png]]: Missing or stale link to 3.6 Documentation from Help Panel in software module
 
−
 
 
−
[[Image:WeakDoc.png]]: Weak or Incomplete 3.6 Documentation
 
−
 
 
  
 
[[Slicer-3.6-QA|Slicer 3.6 QA table]]
 
[[Slicer-3.6-QA|Slicer 3.6 QA table]]
−
 
−
'''Modules'''
 
−
*Please copy the template linked below, paste it into your page and customize it with your module's information.
 
−
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]
 
−
*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:
 
−
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)
 
−
 
−
'''Requirements for Modules'''
 
−
{| 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-3.6#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]]
 
−
|}
 
−
 
−
Please adhere to the naming scheme for the module documentation:
 
−
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)
 

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

Retrieved from "https://www.slicer.org/w/index.php?title=Documentation/3.6&oldid=61787"