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=
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{{documentation/versionlist}}
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 +
=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.
  
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]]
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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 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: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=
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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]].
*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'''
 
*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:
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*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)
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*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>
  
=Requirements for Modules=
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=Main GUI=
{| 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 added since the 3.4 release=
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*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (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: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:StereoViewing-3.6 | Setting up and using stereoscopic viewing ]] (Curt Lisle, Wendy Plesniak)
 +
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)
  
* [[Modules:AtlasCreator-Documentation-3.5|Atlas Creator]] (Sylvain Jaume)  '''Not yet 3.6'''
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=Modules=
* [[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'''
 
  
=List of pre-existing Modules=
 
 
==Core==
 
==Core==
*[[Modules:Camera-Documentation-3.5| Camera Module]] (Sebastian Barre) '''Not yet 3.6'''
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*[[Modules:Welcome-Documentation-3.6| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis)
*[[Modules:Welcome-Documentation-3.4| Welcome Module]] (Wendy Plesniak, Steve Pieper, Sonia Pujol, Ron Kikinis) '''Not yet 3.6'''
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*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)  
*[[Modules:Volumes-Documentation-3.4| Volumes Module]] (Alex Yarmarkovich, Steve Pieper) '''Not yet 3.6'''
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*[[Modules:Volumes-Documentation-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)  
**[[Modules:Volumes:Diffusion Editor-Documentation-3.4| Diffusion Editor]] (Kerstin Kessel) '''Not yet 3.6'''
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**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
*[[Modules:Models-Documentation-3.4| Models Module]] (Alex Yarmarkovich) '''Not yet 3.6'''
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*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)  
*[[Modules:Fiducials-Documentation-3.4| Fiducials Module]] (Nicole Aucoin) '''Not yet 3.6'''
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*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
*[[Modules:Data-Documentation-3.4| Data Module]] (Alex Yarmarkovich'''Not yet 3.6'''
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*[[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper)   
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''Not yet 3.6'''
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*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)  
*[[Modules:Color-Documentation-3.4| Color Module]] (Nicole Aucoin) '''Not yet 3.6'''
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*[[Modules:Fiducials-Documentation-3.6| Fiducials Module]] (Nicole Aucoin)  
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper) '''Not yet 3.6'''
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*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:ROIModule-Documentation-3.4|ROI Module]] (Alex Yarmarkovich) '''Not yet 3.6'''
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*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:VolumeRendering-Documentation-3.5| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich) '''Not yet 3.6'''
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*[[Modules:Transforms-Documentation-3.6| Transforms Module]] (Alex Yarmarkovich)  
 +
*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
  
==Specialized Modules==
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==Wizards==
 +
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
 +
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)
  
Please adhere to the naming scheme for the module documentation:
+
==Informatics Modules==
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)
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*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus) 
 +
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)
  
===Wizards===
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==Registration==
*[[Modules:ChangeTracker-Documentation-3.4|ChangeTracker]] (Andriy Fedorov)  '''Not yet 3.6'''
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*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.
*[[Modules:IA_FEMesh-Documentation-3.4|IA FE Meshing Module]] (Vince Magnotta) '''Not yet 3.6'''
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*[http://www.slicer.org/wiki/Slicer-3-6-FAQ '''Registration FAQ''']
===Informatics Modules===
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*Fast Registration
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak) '''Not yet 3.6'''
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**[[Modules:Transforms-Documentation-3.6|Transforms]]:  manual & interactive rigid registration , (Alex Yarmarkovich)
*[[Modules:QDECModule-Documentation-3.4| QDEC Module]] (Nicole Aucoin'''Not yet 3.6'''
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**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]:  automated fast affine registration , (Jim Miller)  
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak'''Not yet 3.6'''
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**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]:  automated fast rigid (6 DOF) registration , (Jim Miller)   
===Registration===
+
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)   
*[[Slicer3:Registration|Overview of all Registration Modules ]]
+
*Robust Registration
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''
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**[[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|Register Images Multires]] (Casey Goodlett, Stephen Aylward) '''Not yet 3.6'''
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**[[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:FiducialRegistration-Documentation-3.5|Fiducial-Based Registration]] (Casey Goodlett) '''Not yet 3.6'''
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** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).
**[[Modules:Transforms-Documentation-3.4| Transforms Module]] (Alex Yarmarkovich) '''Not yet 3.6'''
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** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek) '''Not yet 3.6'''
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** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]] (Daniel Blezek) '''Not yet 3.6'''
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*Brain Only Registration
**[[Modules:DeformableB-SplineRegistration-Documentation-3.4|Deformable B-Spline Registration]] (Bill Lorensen'''Not yet 3.6'''
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**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along the AC-PC line (Nicole Aucoin)
**[[Modules:DemonsRegistration-Documentation-3.6|Demons Registration]] (Tom Vercauteren) '''Not yet 3.6'''
+
*Non-Raster-Image Data Registration
**[[Modules:RealignVolume-Documentation-3.4|ACPC Transform]] (Nicole Aucoin) '''Not yet 3.6'''
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**[[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)
  
===Segmentation===
+
==Segmentation==
*[[Modules:EMSegment|EM Segment]] (Sylvain Jaume, Nicolas Rannou)  '''Not yet 3.6'''
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*[[Modules:SegmentationOverview3.6|Overview]]
*[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Brad Davis, Will Schroeder'''Not yet 3.6'''
+
**[[Modules:EMSegmenter-3.6|EM Segmenter]] (Kilian Pohl)   
*[[Modules:EMSegment-Simple|EM Segment Simple]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''
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**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching Segmentation]] (Andriy Fedorov)
*[[Modules:EMSegment-TemplateBuilder|EM Segment Template Builder]] (Brad Davis, Will Schroeder) '''Not yet 3.6'''
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**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
*[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller)  '''Not yet 3.6'''
+
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)   
*[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen) '''Not yet 3.6'''
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**[[Modules:RobustStatisticsSeg-Documentation-3.6|Robust Statistics Segmentation]] Yi Gao (yigao@gatech.edu).
 +
**[[Modules:BRAINSROIAuto-Documentation-3.6|BRAINSROIAuto]] Hans Johnson (hans-johnson@uiowa.edu).
 +
**[[Modules:GrowCutSegmentation-Documentation-3.6|Grow Cut Segmentation]] (Harini Veeraraghavan)
  
===Statistics===
+
==Quantification==
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper) '''Not yet 3.6'''
+
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
 +
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)
  
===Diffusion===
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==Diffusion MRI==
====DWI====
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* [[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion MRI Welcome Module]]
*Estimation
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* DWI Denoising
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar)  '''Not yet 3.6'''
+
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)  
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (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)   
*Filter
+
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]]  (Antonio Tristán Vega, Santiago Aja-Fernandez)   
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez) '''Not yet 3.6'''
+
* Diffusion Tensor Utilities
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer)  '''Not yet 3.6'''
+
**[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar) 
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]]  (Antonio Tristán Vega, Santiago Aja-Fernandez)  '''Not yet 3.6'''
+
**[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)   
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal'''Not yet 3.6'''
+
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
*[[Modules:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''
+
* 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)
  
====DTI====
+
==IGT==
*[[Modules:ResampleDTIVolume-Documentation-3.4|Resample DTI Volume]] (Francois Budin) '''Not yet 3.6'''
+
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar) '''Not yet 3.6'''
+
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
*Analysis
+
*[[Modules:ProstateNav-Documentation-3.6| ProstateNav Module]] (Junichi Tokuda, Andras Lasso)
 +
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles)
 +
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)
  
===Tractography===
+
==Time Series==
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)  '''Not yet 3.6'''
+
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)
*[[Modules:FiducialSeeding-Documentation-3.4|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper) '''Not yet 3.6'''
 
*[[Modules:DTIDisplay-Documentation-3.4|FiberBundles]] (Alex Yarmakovich) '''Not yet 3.6'''
 
*[[Modules:StochasticTractography-Documentation-3.4|Python Stochastic Tractography]] (Julien de Siebenthal)  '''Not yet 3.6'''
 
*[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)  '''Not yet 3.6'''
 
  
===IGT===
+
==Filtering==
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda)   '''Not yet 3.6'''
+
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov)
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu) '''Not yet 3.6'''
+
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda) '''Not yet 3.6'''
+
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
===Filtering===
+
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''
+
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich) 
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''
+
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:ImageLabelCombine-3.4|Image Label Combine]] (Alex Yarmarkovich) '''Not yet 3.6'''
+
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)  
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''
+
*[[Registration:Resampling|'''Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)
*[[Modules:ResampleVolume2-Documentation-3.4|Resample Volume2]] (Francois Budin) '''Not yet 3.6'''
+
**[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
*[[Modules:ThresholdImage-Documentation-3.4|Threshold Image]] (Nicole Aucoin) '''Not yet 3.6'''
+
**[[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)
 +
 
 +
==Endoscopy==
 +
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)
 +
 
 +
==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 [[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'''
  
===Surface Models===
+
* Import/Export
*[[Modules:Model_Maker-Documentation-3.4| Modelmaker]] (Nicole Aucoin) '''Not yet 3.6'''
+
** [[Modules:PlastimatchDICOMRT|Plastimatch > DICOM-RT Import]] Greg Sharp (gcsharp@partners.org).
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''
+
* 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)
  
*Freesurfer Surface Section Extraction (Katharina Quintus)
+
:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins
*[[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:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models
*[[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===
+
:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface
*[[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=
+
:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution
  
==Extensions for Downloading==
+
:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures
===Introduction===
+
 
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
+
'''Installation Instructions'''
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
+
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
* Some of the extensions do not use the Slicer license. Please review carefully.
+
[[image:Slicertoolbar.png|Extensions Wizard]]
* 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.
 
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.
 
  
 
[[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'''
 
*Click on the icon to start the extensions wizard
 
[[image:ExtensionsWizard.png|Extensions Wizard]]
 
 
===Listing of available plug-ins===
 
* VMTK Daniel Haehn (haehn@bwh.harvard.edu)
 
* [[Modules:VMTKSlicerModule|VmtkSlicerModule]] Daniel Haehn (haehn@bwh.harvard.edu) Prerequisite install for all VMTK plugins.  '''Not yet 3.6'''
 
 
* [[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface  '''Not yet 3.6'''
 
 
* [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] Daniel Haehn (haehn@bwh.harvard.edu) providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms  '''Not yet 3.6'''
 
 
* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] Daniel Haehn (haehn@bwh.harvard.edu) providing vessel enhancement filters to highlight vasculature or tubular structures  '''Not yet 3.6'''
 
 
* [[Modules:EMDTIClustering-Documentation-3.5|EM DTI Clustering]] Mahnaz Maddah (maddah@ge.com)  '''Not yet 3.6'''
 
  
* [[Modules:LabelDiameterEstimation-Documentation-3.5|Label Diameter Estimation]] Andriy Fedorov (fedorov@bwh.harvard.edu)  '''Not yet 3.6'''
+
'''Info for Developers'''
 +
For explanations for developers see [[Slicer3:Extensions| here]]
  
* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu)  '''Not yet 3.6'''
+
=Other information=
  
* [[Modules:HAMMER]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''
+
'''Developer Tools'''
 +
*[[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
 +
*[[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:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)
  
* [[Modules:BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu)
 
  
* [[Modules:BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu)
+
'''Non-SPL Supported Compatibility Packages'''
 +
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''
  
* [[Modules:BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com) **EXTENSION NO LONGER MAINTAINED**
 
  
* [[Modules:LupusLesion]] Mark Scully (mscully@mrn.org)
+
'''QA Table'''
  
* [[Modules:ARCTIC]] Cedric Mathieu (ced.mathieu@gmail.com)
+
[[Slicer-3.6-QA|Slicer 3.6 QA table]]

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