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]]
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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. 
 +
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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.
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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)
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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]].
 +
 
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*For information on how to use Slicer 3.6 please go to the [[Training|training]] pages.
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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]]
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*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
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*<big>For an overview on how to load your data, see [[Slicer-3.6-Load-Overview|here]]</big>
  
 
=Main GUI=
 
=Main GUI=
  
*[[Modules:MainApplicationGUI-Documentation-3.6| Main Application GUI]] ' (Wendy Plesniak)  
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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)  
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*[[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)
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*[[Modules:SceneSnapshots-3.6| Creating and Restoring Scene Snapshots]] (Wendy Plesniak)
*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)
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*[[Modules:StereoViewing-3.6 | Setting up and using stereoscopic viewing ]] (Curt Lisle, Wendy Plesniak)
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*[[Modules:ExtensionsManagementWizard-Documentation-3.6| Extensions Management Wizard]] (Wendy Plesniak)
  
 
=Modules=
 
=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]]
 
|}
 
  
=List of Modules added or significantly revised since the 3.4 release=
 
* 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 Modules=
 
 
==Core==
 
==Core==
*[[Slicer3:Multiple_Cameras| Camera Module]] (Sebastian Barre)
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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)
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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-3.6| Diffusion Editor]] (Kerstin Kessel)
 
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
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*[[Modules:Slices-Documentation-3.6|Slices Module]] (Jim Miller)
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*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
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*[[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)
*[[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-3.6|Slices Module]] (Jim Miller)  
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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)  <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
 
*[[Modules:ROIModule-Documentation-3.6|ROI Module]] (Alex Yarmarkovich)
 
*[[Modules:VolumeRendering-Documentation-3.6| Volume Rendering Module]] (Yanling Liu, Alex Yarmarkovich)
 
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)
 
 
 
==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===
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==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) <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
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*[[Modules:IA_FEMesh-Documentation-3.6|IA FE Meshing Module]] (Vincent Magnotta, Curt Lisle)
  
===Informatics Modules===
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==Informatics Modules==
 
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)   
 
*[[Modules:FetchMI-Documentation-3.6| Fetch Medical Informatics Module]] (Wendy Plesniak, Dan Marcus)   
*[[Modules:QDECModule-Documentation-3.6| QDEC Module]] (Nicole Aucoin)
 
 
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)
 
*[[Modules:QueryAtlas-Documentation-3.6|Query Atlas Module]] (Wendy Plesniak)
  
===Registration===
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==Registration==
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: go here for more detailed help on selecting your registration module.
+
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.
*Fast
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*[http://www.slicer.org/wiki/Slicer-3-6-FAQ '''Registration FAQ''']
**[[Modules:Transforms-Documentation-3.6|Transforms Module]]:  manual & interactive rigid registration , (Alex Yarmarkovich)
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*Fast Registration
**[[Modules:AffineRegistration-Documentation-3.4|Fast Affine Module]]:  automated fast affine registration , (Daniel Blezek<span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>'
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**[[Modules:Transforms-Documentation-3.6|Transforms]]:  manual & interactive rigid registration , (Alex Yarmarkovich)
**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Non-rigid BSpline Module]]: fast non-rigid registration , (Bill Lorensen)   
+
**[[Modules:AffineRegistration-Documentation-3.6|Fast Affine Registration]]:  automated fast affine registration , (Jim Miller)   
*Robust
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**[[Modules:RigidRegistration-Documentation-3.6|Fast Rigid Registration]]:  automated fast rigid (6 DOF) registration , (Jim Miller) 
**[[Modules:RegisterImages-Documentation-3.6|Robust Rigid-Affine-Nonrigid Module]]:  registration with robust initialization, variable DOF and masking options, (Casey Goodlett)
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**[[Modules:DeformableB-SplineRegistration-Documentation-3.6|Fast Nonrigid BSpline Registration]]: fast non-rigid registration , (Bill Lorensen)   
**[[Modules:RegisterImagesMultiRes-Documentation-3.6|Robust Multiresolution Affine Module]]: affine registration in multi-resolution scheme, robust to large differences in initial position or image content ,  (Casey Goodlett)
+
*Robust Registration
*Brain Only
+
**[[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:ACPCTransform-Documentation-3.6|ACPC Transform Module]]: align a single brain along AC-PC line (Nicole Aucoin)
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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)
*Non-Raster-Image Data
+
** [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu).
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration Module]]: align two sets of fiducials (translation, rigid or similarity)  (Casey Goodlett)
+
** [[Modules:BRAINSFit|BRAINSFit]] Hans Johnson (hans-johnson@uiowa.edu).
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration Module]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek) <span style="background:hotpink; color:white">Not yet 3.6 (in progress)</span><font background=hotpink color=white>Not yet 3.6 (in progress)</font>
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** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).
*Experimental and auxiliary
+
*Brain Only Registration
**[[Modules:RegistrationMetrics-Documentation-3.5 | Registration Metrics (HD and DSC) ]] (Haytham Elhawary)  <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
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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:LinearRegistration-Documentation-3.4|Linear Registration Module]]: (fast) rigid registration m (Daniel Blezek) <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
+
*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)
  
===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)
**[[Modules:Simple Region Growing-Documentation-3.6|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan)  <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
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**[[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).
 +
**[[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-3.6|Label Statistics]] (Steve Pieper)
 
*[[Modules:LabelStatistics-Documentation-3.6|Label Statistics]] (Steve Pieper)
 +
*[[Modules:PETCTFusion-Documentation-3.6 | PET/CT Fusion Module]] (Wendy Plesniak)
  
===Diffusion MRI===
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==Diffusion MRI==
*Diffusion MRI
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* [[Modules:DiffusionMRIWelcome-Documentation-3.6|Diffusion MRI Welcome Module]]
** DWI filtering
+
* DWI Denoising
***[[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)   
***[[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)   
***[[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
***[[Modules:DiffusionTensorEstimation-Documentation-3.6|Diffusion Tensor Estimation]] (Raul San Jose Estepar)   
+
**[[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: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)   
***[[Modules:ROISeeding-Documentation-3.6 | Label Seeding]] (Raul San Jose Estepar)   
+
**[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmarkovich, Steve Pieper)  
***[[Modules:FiducialSeeding-Documentation-3.6|Fiducial Seeding]] (Alex Yarmakovich, Steve Pieper)  
+
**[[Modules:DTIDisplay-Documentation-3.6|FiberBundles]] (Alex Yarmarkovich)  
***[[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)
***[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)
+
* Pipeline
 +
**[[GTRACT_V4 | GTRACT CLI tools]] (Vincent Magnotta)
  
===IGT===
+
==IGT==
 
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
 
*[[Modules:OpenIGTLinkIF-Documentation-3.6| OpenIGTLinkIF Module]] (Junichi Tokuda)
 
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
 
*[[Modules:NeuroNav-Documentation-3.6| NeuroNav Module]] (Haiying Liu)
Line 143: Line 118:
 
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)
 
*[[Modules:IGTToolSelector-Documentation-3.6 | IGT Tool Selector ]] (Andrew Wiles)
  
===Time Series===
+
==Time Series==
 
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)
 
* [[Modules:FourDImage-Documentation-3.6|4D Image (Viewer)]] (Junichi Tokuda)
  
===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: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-3.4|Histogram Matching]] (Bill Lorensen, Xiaodong Tao)
+
*[[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-3.6|Resample Volume]] (Bill Lorensen)
 
*[[Modules:ResampleScalarVectorDWIVolume-Documentation-3.6|Resample Scalar/Vector/DWI Volume]] (Francois Budin)
 
 
*[[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)  
 
**[[Modules:SubtractImages-Documentation-3.6|Subtract Images]] (Harini Veeraraghavan)   
 
**[[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-3.6|Mask Image]] (Nicole Aucoin, Harini Veeraraghavan)  
+
** [[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) <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
+
**[[Modules:GradientAnisotropicFilter-Documentation-3.6| Gradient Anisotropic Filter]]  (Bill Lorensen)
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.4|Curvature Anisotropic Diffusion]] (Bill Lorensen) <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
+
**[[Modules:CurvatureAnisotropicDiffusion-Documentation-3.6|Curvature Anisotropic Diffusion]] (Bill Lorensen)
**[[Modules:GaussianBlur-Documentation-3.4|Gaussian Blur]] (Julien Jomier, Stephen Aylward) <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
+
**[[Modules:GaussianBlur-Documentation-3.6|Gaussian Blur]] (Julien Jomier, Stephen Aylward)
**[[Modules:MedianFilter-Documentation-3.4|Median Filter]] (Xiaodong Tao)  <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
+
**[[Modules:MedianFilter-Documentation-3.6|Median Filter]] (Xiaodong Tao)   
 
*Morphology
 
*Morphology
**[[Modules:VotingBinaryHoleFilling-Documentation-3.4|Voting Binary Hole Filling]] (Jim Miller)  <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
+
**[[Modules:VotingBinaryHoleFilling-Documentation-3.6|Voting Binary Hole Filling]] (Jim Miller)   
 
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
 
**[[Modules:GrayscaleFillHole-Documentation-3.6|Grayscale Fill Hole]] (Bill Lorensen)
 
**[[Modules:GrayscaleGrindPeak-Documentation-3.6|Grayscale Grind Peak]] (Bill Lorensen)
 
**[[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)  
*[[Modules:GrayscaleModelMaker-Documentation-3.6|Grayscale Model Maker]] (Bill Lorensen) <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
+
*[[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-3.6| Python Surface Connectivity]] (Luca Antiga, Daniel Blezek) <span style="background:hotpink; color:white">Not yet 3.6 (in progress)</span><font background=hotpink color=white>Not yet 3.6 (in progress)</font>
+
*[[Modules:PythonSurfaceConnectivity-Documentation-3.6| Surface Connectivity]] (Luca Antiga, Daniel Blezek)
*[[Modules:PythonSurfaceICPRegistration-Documentation-3.6| Python Surface ICP Registration]] (Luca Antiga, Daniel Blezek)  <span style="background:hotpink; color:white">Not yet 3.6 (in progress)</span><font background=hotpink color=white>Not yet 3.6 (in progress)</font>
+
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Surface Toolbox]] (Luca Antiga, Daniel Blezek)  
*[[Modules:PythonSurfaceToolbox-Documentation-3.6| Python Surface Toolbox]] (Luca Antiga, Daniel Blezek)   <span style="background:hotpink; color:white">Not yet 3.6 (in progress)</span><font background=hotpink color=white>Not yet 3.6 (in progress)</font>
 
 
*[[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-3.6|Create a Dicom Series]] '''(in progress)''' (Xiaodong Tao) 
 
*[[Modules:DicomToNRRD-3.6|Dicom to NRRD]] '''(in progress)''' (Xiaodong Tao)
 
*[[Modules:OrientImages-Documentation-3.4|Orient Images]] (Xiaodong Tao)  <span style="background:hotpink; color:white">Not yet 3.6</span><font background=hotpink color=white>Not yet 3.6</font>
 
*[[Modules:PythonExplodeVolumeTransform-Documentation-3.6| Python Explode Volume Transform]] (Luca Antiga, Daniel Blezek)  <span style="background:hotpink; color:white">Not yet 3.6 (in progress)</span><font background=hotpink color=white>Not yet 3.6 (in progress)</font>
 
 
*[[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 cogwheel icon to start the extensions wizard (highlighted in red)
 
[[image:Slicertoolbar.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'''. Belongs to segmentation
+
* Import/Export
 
+
** [[Modules:PlastimatchDICOMRT|Plastimatch > DICOM-RT Import]] Greg Sharp (gcsharp@partners.org).
* [[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'''. Belongs to wizards
+
* Segmentation
 
+
** [[Modules:ABC-Documentation-3.5|ABC]] Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) '''Not yet 3.6'''.  
* [[Modules:BRAINSDemonWarp|BRAINSDemonWarp]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration, robust
+
** [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox at research.ge.com) .
 
+
** [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).  
* [[Modules:BRAINSFit|BRAINSFit]] Eun Young Kim (eunyoung-kim@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust
+
** [[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)
* [[Modules:BRAINSMush|BRAINSMush]] Hans Johnson (hans-johnson@uiowa.edu) '''Not yet 3.6'''. Belongs to registration robust.
+
* Registration
 
+
**Robust
* [[Modules:CMTK|CMTK]] Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com) '''Not yet 3.6'''. Belongs to 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:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) '''Not yet 3.6'''. Belongs to tractography
+
** [[Modules:Plastimatch|Plastimatch > B-spline deformable registration]] Greg Sharp (gcsharp@partners.org).
 
+
** [[Modules:PlastimatchLANDWARP|Plastimatch > Landmark-based registration]] Nadya Shusharina (nshusharina@partners.org).  
* [[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:PlastimatchXFORMWARP|Plastimatch > Warping with transform]] Nadya Shusharina, Greg Sharp (gcsharp@partners.org)
 
+
* Wizards
* [[Modules:FuzzySegmentationModule|FuzzySegmentationModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to segmentation.
+
** [[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) .
* [[Modules:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) '''Not yet 3.6'''. Belongs to registration robust.
+
* Tractography
 
+
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).
* [[Modules:LabelDiameterEstimation-Documentation-3.5|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) '''Not yet 3.6'''. Belongs to IGT.
+
* DWI
 
+
** [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) .
* [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) '''Not yet 3.6'''. Belongs to wizards.
+
* 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:Plastimatch|Plastimatch]] Greg Sharp (gcsharp@partners.org) '''Not yet 3.6'''. Belongs to registration robust.
+
* Quantification
 
+
** [[Modules:LabelDiameterEstimation-Documentation-3.6|LabelDiameterEstimation]] Andriy Fedorov (fedorov@bwh.harvard.edu) .  
* [[Modules:RicianNoiseFilter|RicianNoiseFilter]] Ross Whitaker (whitaker@cs.utah.edu) '''Not yet 3.6'''. Belongs to DWI
+
* [[Image:Slicervmtk_logo.png|right|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)
 
 
* [[Modules:SkullStripperModule|SkullStripperModule]] Xiaodong Tao (taox@research.ge.com) '''Not yet 3.6'''. Belongs to wizards
 
 
 
* [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu). Belongs to wizards
 
 
 
* [[Image:Slicervmtk_logo.png|150px]] The Vascular Modeling Toolkit in 3D Slicer, Daniel Haehn (haehn@bwh.harvard.edu)
 
  
 
:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins
 
:*[[Modules:VMTKSlicerModule|VmtkSlicerModule]] prerequisite install for all VMTK plug-ins
Line 270: Line 225:
 
:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures
 
:*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures
  
 +
'''Installation Instructions'''
 +
*Click on the cogwheel icon to start the extensions wizard (highlighted in red)
 +
[[image:Slicertoolbar.png|Extensions Wizard]]
  
====Example Extensions====
 
  
* [[Modules:ExampleCommandLine|ExampleCommandLine]] Jim Miller '''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: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'''
+
'''Info for Developers'''
 +
For explanations for developers see [[Slicer3:Extensions| here]]
  
* [[Modules:TclSampleScriptedModule|TclSampleScriptedModule]] Steve Pieper '''Not yet 3.6'''
+
=Other information=
  
 +
'''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)
  
  
 
'''Non-SPL Supported Compatibility Packages'''
 
'''Non-SPL Supported Compatibility Packages'''
 +
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''
 +
  
* [[Modules:BioImageSuite|BioImageSuite]] Xenios Papademtrios '''Not yet 3.6'''
+
'''QA Table'''
  
=QA=
 
 
[[Slicer-3.6-QA|Slicer 3.6 QA table]]
 
[[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