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=
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 +
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.
 +
 
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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:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
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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]].
*[[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:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]]  (Wendy Plesniak)
 
  
=Modules=
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*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.
*Please copy the template linked below, paste it into your page and customize it with your module's information.
+
*For information on how to obtain Slicer 3.6 please go to the [http://www.slicer.org/pages/Special:SlicerDownloads Download Pages].
[[Slicer3:Module_Documentation-3.6_Template|Slicer3:Module_Documentation-3.6_Template]]  
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*For sample data see [[SampleData|here]]
*See Requirements for Modules for info to be put into the Help and Acknowledgment Tabs
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*For documentation on other versions of Slicer see [[Documentation|here]]
*To put your lab's logo into a module, see [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3|here]]
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*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>
  
Please adhere to the naming scheme for the module documentation:
+
=Main GUI=
*[ [Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)
 
  
=Requirements for Modules=
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*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] (Wendy Plesniak)
{| border="00" cellpadding="5" cellspacing="0"
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*[[Modules:EventBindings-3.6| "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)
|-
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*[[Modules:Loading-Data-3.6| Loading Data]] (scenes, DICOM, volumes, models, fiducials, transforms, etc.(Wendy Plesniak)
| rowspan="2"|
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*[[Modules:Saving-Documentation-3.6| Saving Data]] (scenes, volumes, models, fiducials, transforms, etc.) (Wendy Plesniak)
* The module is '''feature complete''', it does everything that it advertises it can do
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*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.
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*[[Modules:StereoViewing-3.6 | Setting up and using stereoscopic viewing ]] (Curt Lisle, Wendy Plesniak)
* 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.
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*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)
*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 or significantly revised since the 3.4 release=
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=Modules=
* Interactive Editor
 
* Volume Rendering
 
* Colors (Nicole Aucoin)
 
* MRI Bias Field Correction (Sylvain Jaume)
 
* 4D Image (Viewer) (Junichi Tokuda)
 
* 4D Analysis (Time-intensity curve plotting and analysis) (Junichi Tokuda)
 
* Fast Marching segmentation (Andriy Fedorov)
 
* Mesh Contour Segmentation]] (Peter Karasev)
 
* Subvolume extraction with ROI widget (Andriy Fedorov)
 
* Registration Metrics (HD and DSC) (Haytham Elhawary)
 
* Measurements (rulers and angles) (Nicole Aucoin)
 
* Affine registration (Casey Goodlett)
 
* Collect Patient Fiducials (Andrew Wiles)
 
* IGT Tool Selector (Andrew Wiles)
 
* Fiducials (Nicole Aucoin)
 
  
=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-3.6| Volumes Module]] (Alex Yarmarkovich, Steve Pieper)  
 
*[[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:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
 +
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
 +
*[[Modules:Editor-Documentation-3.6|Editor]] (Steve Pieper) 
 
*[[Modules:Models-Documentation-3.6| Models Module]] (Alex Yarmarkovich)  
 
*[[Modules: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-3.5 | Measurements (rulers and angles) ]] (Nicole Aucoin) [[Modules:Measurements-Documentation-3.6 | '''3.6 in progress''']]
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*[[Modules:Measurements-Documentation-3.6 | Measurements (rulers and angles) ]] (Nicole Aucoin)
*[[Modules:Data-Documentation-3.6| Data Module]] (Alex Yarmarkovich)  
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*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
*[[Modules:Slices-Documentation-3.4|Slices Module]] (Jim Miller) '''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)
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*[[Modules:Colors-Documentation-3.6| Color Module]] (Nicole Aucoin)
*[[Modules:Editor-Documentation-3.4| Interactive Editor]] (Steve Pieper)  '''Not yet 3.6'''
 
*[[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'''
 
 
 
==Specialized Modules==
 
 
 
Please adhere to the naming scheme for the module documentation:
 
*[[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)
 
  
===Wizards===
+
==Wizards==
 
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
 
*[[Modules:ChangeTracker-Documentation-3.6|ChangeTracker]] (Andriy Fedorov)
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta) '''3.6 In Progress'''
+
*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)
 
 
===Informatics Modules===
 
*[[Modules:FetchMI-Documentation-3.4| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)  '''Not yet 3.6'''
 
*[[Modules:QDECModule-Documentation-3.6| QDEC Module]] (Nicole Aucoin)
 
*[[Modules:QueryAtlas-Documentation-3.4|Query Atlas Module]] (Wendy Plesniak)  '''Not yet 3.6'''
 
 
 
===Registration===
 
*[[Slicer3:Registration|Overview of all Registration Modules ]]
 
**[[Modules:RegisterImages-Documentation-3.6|Register Images (''Upgraded Version'')]] (Casey Goodlett)
 
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Register Images Robust Affine]] (Casey Goodlett)
 
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Deformable B-Spline Registration]] (Bill Lorensen)  '''in progress'''
 
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial-Based Registration]] (Casey Goodlett)
 
**[[Modules:Transforms-Documentation-3.6| Transforms Module for interactive rigid registration]] (Alex Yarmarkovich)
 
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]] (Nicole Aucoin)
 
**[[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary)  '''Not yet 3.6'''
 
**[[Modules:LinearRegistration-Documentation-3.4|Linear Registration]] (Daniel Blezek)  '''Not yet 3.6'''
 
**[[Modules:AffineRegistration-Documentation-3.4|Affine Registration]]  (Daniel Blezek)  '''Not yet 3.6'''
 
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)  '''Not yet 3.6'''
 
 
 
===Segmentation===
 
*Overview (Kilian)
 
**[[Modules:EMSegment|EM Segment]] (Kilian Pohl)  '''Not yet 3.6'''
 
**[[Modules:EMSegment-Command-Line|EM Segment Command-Line]] (Kilian Pohl)  '''Not yet 3.6'''
 
**[[Modules:EMSegment-Simple|EM Segment Simple]] (Kilian Pohl)  '''Not yet 3.6'''
 
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching segmentation]] (Andriy Fedorov)
 
**[[Modules:OtsuThreshold-Documentation-3.4|Otsu Threshold]] (Bill Lorensen)  '''Not yet 3.6'''
 
**[[Modules:Simple Region Growing-Documentation-3.4|Simple Region Growing]] (Jim Miller) '''Not yet 3.6'''
 
  
===Statistics===
+
==Informatics Modules==
*[[Modules:LabelStatistics-Documentation-3.4|Label Statistics]] (Steve Pieper'''Not yet 3.6'''
+
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)   
 +
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)
  
===Diffusion===
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==Registration==
====DWI====
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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.
*Estimation
+
*[http://www.slicer.org/wiki/Slicer-3-6-FAQ '''Registration FAQ''']
**[[Modules:DiffusionTensorEstimation-Documentation-3.4|Diffusion Tensor Estimation]] (Raul San Jose Estepar) '''Not yet 3.6'''
+
*Fast Registration
*[[Modules:PythonExtractBaseline-Documentation-3.4|Python Extract Baseline DWI Volume]] (Julien de Siebenthal'''Not yet 3.6'''
+
**[[Modules:Transforms-Documentation-3.6|Transforms]]:  manual & interactive rigid registration , (Alex Yarmarkovich)
*Filter
+
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]:  automated fast affine registration , (Jim Miller) 
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.4|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)  '''Not yet 3.6'''
+
**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]:  automated fast rigid (6 DOF) registration , (Jim Miller)   
**[[Modules:RicianLMMSEImageFilter-Documentation-3.4|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer) '''Not yet 3.6'''
+
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen) 
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.4|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)  '''Not yet 3.6'''
+
*Robust Registration
*[[Modules:ShiftDWIValues-Documentation-3.4|Python Shift DWI Values]] (Julien de Siebenthal'''Not yet 3.6'''
+
**[[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:RecenterScalar2DWI-Documentation-3.4|Python Recenter Scalar to DWI Volume]] (Julien de Siebenthal) '''Not yet 3.6'''
+
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Registration]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content ,  (Casey Goodlett)
 +
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).
 +
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).
 +
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).
 +
*Brain Only Registration
 +
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along the AC-PC line (Nicole Aucoin)
 +
*Non-Raster-Image Data Registration
 +
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity(Casey Goodlett)
 +
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)
 +
* [[Modules:AtlasCreator|Atlas Creator]]: create a statistical atlas (Daniel Haehn, Kilian Pohl)
  
====DTI====
+
==Segmentation==
*[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
+
*[[Modules:SegmentationOverview3.6|Overview]]
*[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar'''Not yet 3.6'''
+
**[[Modules:EMSegmenter-3.6|EM Segmenter]] (Kilian Pohl) 
*Analysis
+
**[[Modules:FastMarchingSegmentation-Documentation-3.6|Fast Marching Segmentation]] (Andriy Fedorov)
 +
**[[Modules:OtsuThresholdSegmentation-Documentation-3.6|Otsu Threshold Segmentation]] (Bill Lorensen)
 +
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)   
 +
**[[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)
  
====Tractography====
+
==Quantification==
*[[Modules:ROISeeding-Documentation-3.4 | Label Seeding]] (Raul San Jose Estepar)  '''Not yet 3.6'''
+
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
*[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)  
+
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)
*[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmakovich)
 
*[[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===
+
==Diffusion MRI==
*[[Modules:OpenIGTLinkIF-Documentation-3.4| OpenIGTLinkIF Module]] (Junichi Tokuda'''Not yet 3.6'''
+
* [[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion MRI Welcome Module]]
*[[Modules:NeuroNav-Documentation-3.4| NeuroNav Module]] (Haiying Liu'''Not yet 3.6'''
+
* DWI Denoising
*[[Modules:ProstateNav-Documentation-3.4| ProstateNav Module]] (Junichi Tokuda'''Not yet 3.6'''
+
**[[Modules:JointRicianLMMSEImageFilter-Documentation-3.6|Joint Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez)   
*[[Modules:CollectFiducials-Documentation-3.6 | Collect Patient Fiducials ]] (Andrew Wiles) '''Not yet 3.6'''
+
**[[Modules:RicianLMMSEImageFilter-Documentation-3.6|Rician LMMSE Image Filter]] (Antonio Tristán Vega, Santiago Aja-Fernandez, Marc Niethammer, C-F Westin) 
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles) '''Not yet 3.6'''
+
**[[Modules:UnbiasedNonLocalMeans-Documentation-3.6|Unbiased Non Local Means filter for DWI]] (Antonio Tristán Vega, Santiago Aja-Fernandez)   
 +
* Diffusion Tensor Utilities
 +
**[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar) 
 +
**[[Modules:DiffusionTensorScalarMeasurements-Documentation-3.6 | Diffusion Tensor Scalar Measurements]] (Raul San Jose Estepar)   
 +
**[[Modules:ResampleDTIVolume-Documentation-3.6|Resample DTI Volume]] (Francois Budin)
 +
* Tractography
 +
**[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar) 
 +
**[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmarkovich, Steve Pieper)  
 +
**[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmarkovich)
 +
**[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Ryan Eckbo)  
 +
**[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)
 +
* Pipeline
 +
**[[GTRACT_V4 | GTRACT CLI tools]] (Vincent Magnotta)
  
 +
==IGT==
 +
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
 +
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
 +
*[[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)
  
===Time Series===
+
==Time Series==
* [[Modules:FourDImage-Documentation-3.5|4D Image (Viewer)]] (Junichi Tokuda) '''Not yet 3.6'''
+
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)
* [[Modules:FourDAnalysis-Documentation-3.5|4D Analysis (Time-intensity curve plotting and analysis)]] (Junichi Tokuda)  '''Not yet 3.6'''
 
  
===Filtering===
+
==Filtering==
*[[Modules:MRIBiasFieldCorrection-Documentation-3.5|MRI Bias Field Correction]] (Sylvain Jaume)
+
*[[Modules:N4ITKBiasFieldCorrection-Documentation-3.6|N4 Bias Field Correction]] (Andriy Fedorov)
*[[Modules:CheckerboardFilter-Documentation-3.4|Checkerboard Filter]] (Bill Lorensen) '''Not yet 3.6'''
+
*[[Modules:MRIBiasFieldCorrection-Documentation-3.6|MRI Bias Field Correction]] (Sylvain Jaume)
*[[Modules:HistogramMatching-Documentation-3.4|Histogram Matching]] (Bill Lorensen) '''Not yet 3.6'''
+
*[[Modules:CheckerboardFilter-Documentation-3.6|Checkerboard Filter]] (Bill Lorensen, Jim Miller)
 +
*[[Modules:HistogramMatching-Documentation-3.6|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
 
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)   
 
*[[Modules:ImageLabelCombine-3.6|Image Label Combine]] (Alex Yarmarkovich)   
*[[Modules:ResampleVolume-Documentation-3.4|Resample Volume]] (Bill Lorensen) '''Not yet 3.6'''
+
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
+
*[[Modules:OtsuThreshold-Documentation-3.6|Otsu Threshold]] (Bill Lorensen)  
*[[Modules:ThresholdImage-Documentation-3.6|Threshold Image]] (Nicole Aucoin)
+
*[[Registration:Resampling|'''Resampling Tools''']]: available resampling methods, including tools to resample in place (e.g. change resolution or voxel anisotropy etc.)
 +
**[[Modules:ResampleVolume-Documentation-3.6|Resample Volume]] (Bill Lorensen)
 +
**[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
 +
**[[Modules:ModelTransform-Documentation-3.6|Model Transform]]: "Resample triangulated surface models" (Alex Yarmarkovich)
 
*Arithmetic
 
*Arithmetic
**[[Modules:AddImages-Documentation-3.4|Add Images]] (Bill Lorensen) '''Not yet 3.6'''
+
**[[Modules:AddImages-Documentation-3.6|Add Images]] (Harini Veeraraghavan)  
**[[Modules:SubtractImages-Documentation-3.4|Subtract Images]] (Bill Lorensen'''Not yet 3.6'''
+
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)   
 
** [[Modules:CastImage-Documentation-3.6|Cast Image]] (Nicole Aucoin)  
 
** [[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===
+
==Surface Models==
 
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)  
 
*[[Modules:ModelMaker-Documentation-3.6| ModelMaker]] (Nicole Aucoin)  
*Grayscale Model Maker (Bill Lorensen) '''Not yet 3.6'''
+
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen)
 
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)   
 
*[[Modules:MeshContourSegmentation-Documentation-3.6|Mesh Contour Segmentation]] (Peter Karasev)   
*[[Modules:PythonSurfaceConnectivity-Documentation-3.4| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
+
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.4| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)  '''Not yet 3.6'''
+
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Surface Toolbox]] (Luca Antiga, Daniel Blezek)  
*[[Modules:PythonSurfaceToolbox-Documentation-3.4| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek) '''Not yet 3.6'''
 
 
*[[Modules:ClipModel-Documentation-3.6| Clip Model]] (Alex Yarmarkovich)   
 
*[[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:ModelMirror-Documentation-3.6| Model Mirror]] (Wendy Plesniak)
 +
*[[Modules:PolyDatToLabelmap-Documentation-3.6| PolyDataToLabelmap]] (Xiaodong Tao, Nicole Aucoin)
  
===Batch processing===
+
==Converters==
*[[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:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
 
*[[Modules:ResampleVolumeBatch-Documentation-3.6|Resample Volume batch]] (Julien Finet)
 
 
 
===Converters===
 
*[[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:CropVolume-Documentation-3.6|Crop Volume]] (previously ExtractSubvolumeROI) (Andriy Fedorov)
 
*[[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)
  
=Slicer Extensions=
+
==Endoscopy==
 +
* [[Modules:Endoscopy-Documentation-3.6|Virtual Endoscopy]] (Steve Pieper)
  
==Extensions for Downloading==
+
==Slicer Extensions==
===Introduction===
 
[[Image:SlicerOnNITRC2009.png|thumb|right|Slicer on NITRC]]
 
* Slicer Extensions are a mechanism for third parties to provide modules which extend the functionality of 3d Slicer.
 
* Some of the extensions do not use the Slicer license. Please review carefully.
 
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. In case of problems with those modules, please talk directly to the developers of the extensions.
 
* The version that is available through the extension manager is chosen by the developer of that extension 
 
  
We are using NITRC as the primary repository for contributed extensions. As a general rule, we do not test the extensions ourselves. Use them at your own risk.
 
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]]
 
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.
 
  
 +
'''Introduction'''
  
*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]]
+
* 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]].
  
'''Installation'''
 
*Click on the icon to start the extensions wizard
 
[[image:ExtensionsWizard.png|Extensions Wizard]]
 
 
===Listing of plug-ins===
 
  
 
'''Available Extensions'''
 
'''Available Extensions'''
  
* [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''
+
* Import/Export
 +
** [[Modules:PlastimatchDICOMRT|Plastimatch > DICOM-RT Import]] Greg Sharp (gcsharp@partners.org).
 +
* Segmentation
 +
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.
 +
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .
 +
** [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).
 +
** [[Modules:SkullStripperModule|SkullStripperModule]] '''(in progress)''' Xiaodong Tao (taox AT research.ge.com).
 +
** [[Modules:SPECTRE-Documentation-3.6|SPECTRE]] '''(in progress)''' Nicole Aucoin (nicole@bwh.harvard.edu), Min Chen (mchen55@jhu.edu)
 +
* Registration
 +
**Robust
 +
*** [[Modules:CMTK|CMTK]] Torsten Rohlfing (torsten@synapse.sri.com) (a.k.a. Computational Morphometry Toolkit) 
 +
*** [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).
 +
** [[Modules:Plastimatch|Plastimatch > B-spline deformable registration]] Greg Sharp (gcsharp@partners.org).
 +
** [[Modules:PlastimatchLANDWARP|Plastimatch > Landmark-based registration]] Nadya Shusharina (nshusharina@partners.org).
 +
** [[Modules:PlastimatchXFORMWARP|Plastimatch > Warping with transform]] Nadya Shusharina, Greg Sharp (gcsharp@partners.org)
 +
* Wizards
 +
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .
 +
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mark-scully[at]uiowa[dot]edu) (a.k.a. 3DSlicerLupusLesionModule) .
 +
* Tractography
 +
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).
 +
* DWI
 +
** [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
 +
* Time Series
 +
** [[Modules:FourDAnalysis-Documentation-3.6|4D Analysis (Time-series plotting and analysis including kinetic analysis of DCE MRI)]] Junichi Tokuda (tokuda@bwh.harvard.edu)
 +
* Quantification
 +
** [[Modules:LabelDiameterEstimation-Documentation-3.6|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .
 +
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)
  
* [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) '''Not yet 3.6'''
+
:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins
  
* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''
+
:*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models
  
* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''
+
:*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface
  
* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''
+
:*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution
  
* [[Modules:BRAINSROIAuto|BRAINSROIAuto]] Greg Harris (gregory-harris@uiowa.edu) '''Not yet 3.6'''
+
:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures
  
* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Thorsten Rolfry '''Not yet 3.6'''
+
'''Installation Instructions'''
 +
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
 +
[[image:Slicertoolbar.png|Extensions Wizard]]
  
* [[Modules:EMDTIClustering-Documentation-3.5|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''
 
  
* [[Modules:FourDAnalysis|FourDAnalysis]] Junichi Tokuda (tokuda@bwh.harvard.edu) '''Not yet 3.6'''
+
[[Image:Slicer-3.4.1-extension-manager-2009-10-02.png|thumb|right|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.
  
* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''
 
  
* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''
 
  
* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''
+
'''Info for Developers'''
 +
For explanations for developers see [[Slicer3:Extensions| here]]
  
* [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''
+
=Other information=
  
* [[Modules:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''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:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''
 
  
* [[Modules:RobustStatisticsSeg|RobustStatisticsSeg]] Yi Gao (yigao@gatech.edu) '''Not yet 3.6'''
+
'''Non-SPL Supported Compatibility Packages'''
 
+
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''
* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''
 
 
 
* [[Modules:SpineSegmentation|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu) '''Not yet 3.6'''
 
 
 
* [[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins, Daniel Haehn (haehn@bwh.harvard.edu)
 
 
 
* [[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models, Daniel Haehn (haehn@bwh.harvard.edu) '''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]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution, Daniel Haehn (haehn@bwh.harvard.edu)
 
  
* [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures, Daniel Haehn (haehn@bwh.harvard.edu)
+
'''QA Table'''
  
 
+
[[Slicer-3.6-QA|Slicer 3.6 QA table]]
====Example Extensions====
 
 
 
* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''Not yet 3.6'''
 
 
 
* [[Modules:ExampleLoadableGuiLessModule|ExampleLoadableGuiLessModule]] Steve Pieper '''Not yet 3.6'''
 
 
 
* [[Modules:ExampleLoadableModule|ExampleLoadableModule]] Steve Pieper '''Not yet 3.6'''
 
 
 
* [[Modules:PythonSampleScriptedModule|PythonSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''
 
 
 
* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''
 
 
 
 
 
 
 
'''Deprecated Extensions'''
 
 
 
* [[Modules:BubbleMaker|BubbleMaker]] Carlos Mendoza (carlos.sanchez.mendoza@gmail.com) '''Not yet 3.6'''
 
 
 
 
 
 
 
'''Non-SPL Supported Compatibility Packages'''
 
 
 
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''
 

Latest revision as of 17:05, 21 November 2019

Home < Documentation < 3.6

For the latest Slicer documentation, visit the 4.10 page.

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