Difference between revisions of "Documentation/3.6"

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<noinclude>{{documentation/versioncheck}}</noinclude>
 
[[image:Slicer3-6Announcement-v2.png| right |3.6 Icon]]
 
[[image:Slicer3-6Announcement-v2.png| right |3.6 Icon]]
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{{documentation/versionlist}}
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=Introduction=
 
=Introduction=
  
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*For documentation on other versions of Slicer see [[Documentation|here]]
 
*For documentation on other versions of Slicer see [[Documentation|here]]
 
*For a [[Slicer-3-6-FAQ|FAQ]] see here
 
*For a [[Slicer-3-6-FAQ|FAQ]] see here
 +
*[[Slicer3:Build_Instructions|Slicer version 3 build instructions]] for developers
 
*<big>For an overview on how to load your data, see [[Slicer-3.6-Load-Overview|here]]</big>
 
*<big>For an overview on how to load your data, see [[Slicer-3.6-Load-Overview|here]]</big>
  
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==Registration==
 
==Registration==
 
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.
 
*[[Slicer3:Registration|'''Overview of all Registration Modules''' ]]: This page provides guidance for selecting the module that is optimal for your task.
*[[Slicer3:FAQ#Registration| Slicer3 Registration FAQ]]
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*[http://www.slicer.org/wiki/Slicer-3-6-FAQ '''Registration FAQ''']
*[http://www.slicer.org/slicerWiki/index.php/Slicer-3-6-FAQ '''Registration FAQ''']
 
 
*Fast Registration
 
*Fast Registration
 
**[[Modules:Transforms-Documentation-3.6|Transforms]]:  manual & interactive rigid registration , (Alex Yarmarkovich)
 
**[[Modules:Transforms-Documentation-3.6|Transforms]]:  manual & interactive rigid registration , (Alex Yarmarkovich)
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** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).
 
** [[Modules:BRAINSResample|BRAINSResample]] Hans Johnson (hans-johnson@uiowa.edu).
 
*Brain Only Registration
 
*Brain Only Registration
**[[Modules:ACPCTransform-Documentation-3.6|ACPC Transform]]: calculate a transformation to align a single brain along theh AC-PC line (Nicole Aucoin)
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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)
 
*Non-Raster-Image Data Registration
 
*Non-Raster-Image Data Registration
 
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity)  (Casey Goodlett)
 
**[[Modules:TransformFromFiducials-Documentation-3.6|Fiducial Registration]]: align two sets of fiducials (translation, rigid or similarity)  (Casey Goodlett)
 
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)
 
**[[Modules:PythonSurfaceICPRegistration-Documentation-3.6|Surface Registration]]: automated surface-to-surface (model) registration (Luca Antiga, Daniel Blezek)
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* [[Modules:AtlasCreator|Atlas Creator]]: create a statistical atlas (Daniel Haehn, Kilian Pohl)
  
 
==Segmentation==
 
==Segmentation==
 
*[[Modules:SegmentationOverview3.6|Overview]]
 
*[[Modules:SegmentationOverview3.6|Overview]]
 
**[[Modules:EMSegmenter-3.6|EM Segmenter]] (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: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)
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**[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Ryan Eckbo)   
 
**[[Modules:StochasticTractography-Documentation-3.6|Python Stochastic Tractography]] (Ryan Eckbo)   
 
**[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)
 
**[[Modules:ROISelect-Documentation-3.6|ROI Select]] (Lauren O'Donnell)
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* Pipeline
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**[[GTRACT_V4 | GTRACT CLI tools]] (Vincent Magnotta)
  
 
==IGT==
 
==IGT==
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** [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).  
 
** [[Modules:SpineSegmentation-Documentation-3.6|SpineSegmentation]] Sylvain Jaume (sylvain@csail.mit.edu).  
 
** [[Modules:SkullStripperModule|SkullStripperModule]] '''(in progress)''' Xiaodong Tao (taox AT research.ge.com).  
 
** [[Modules:SkullStripperModule|SkullStripperModule]] '''(in progress)''' Xiaodong Tao (taox AT research.ge.com).  
 +
** [[Modules:SPECTRE-Documentation-3.6|SPECTRE]] '''(in progress)''' Nicole Aucoin (nicole@bwh.harvard.edu), Min Chen (mchen55@jhu.edu)
 
* Registration
 
* Registration
 
**Robust
 
**Robust
 
*** [[Modules:CMTK|CMTK]] Torsten Rohlfing (torsten@synapse.sri.com) (a.k.a. Computational Morphometry Toolkit)   
 
*** [[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:HammerRegistration|HammerRegistration]] GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu).  
*** [[Modules:Plastimatch|Plastimatch > B-spline deformable registration]] Greg Sharp (gcsharp@partners.org).
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** [[Modules:Plastimatch|Plastimatch > B-spline deformable registration]] Greg Sharp (gcsharp@partners.org).
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** [[Modules:PlastimatchLANDWARP|Plastimatch > Landmark-based registration]] Nadya Shusharina (nshusharina@partners.org).
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** [[Modules:PlastimatchXFORMWARP|Plastimatch > Warping with transform]] Nadya Shusharina, Greg Sharp (gcsharp@partners.org)
 
* Wizards
 
* Wizards
 
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .  
 
** [[Modules:ARCTIC-Documentation-3.6|ARCTIC]] Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) .  
** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mscully@mrn.org) (a.k.a. 3DSlicerLupusLesionModule) .
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** [[Modules:LesionSegmentationApplications-Documentation-3.6|LesionSegmentationApplications]] Mark Scully (mark-scully[at]uiowa[dot]edu) (a.k.a. 3DSlicerLupusLesionModule) .
 
* Tractography
 
* Tractography
 
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).
 
** [[Modules:EMDTIClustering-Documentation-3.6|EMFiberClusteringModule]] Mahnaz Maddah (mmaddah@alum.mit.edu) (a.k.a. Quantitative Diffusion Tools).
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*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
 
*[[Modules:Cameras-Documentation-3.6| Camera Module]] (Sebastian Barre)
 
*Note: most developer tools are not documented for end users, but contain comments in the source code
 
*Note: most developer tools are not documented for end users, but contain comments in the source code
 
*[[Modules:EMSegmentBatch-Documentation-3.6|EM Segmenter batch]] (Julien Jomier, Brad Davis)
 
 
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
 
*[[Modules:GaussianBlurBatch-Documentation-3.6|Gaussian Blur batch]] (Julien Jomier, Stephen Aylward)
 
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)
 
*[[Modules:RegisterImagesBatch-Documentation-3.6|Register Images batch]] (Julien Finet, Stephen Aylward)

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