Difference between revisions of "Documentation/3.6"

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*[[Modules:Welcome-Documentation-3.4| 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)
*[[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'''
**[[Modules:Volumes:Diffusion Editor-Documentation-3.6| Diffusion Editor]] (Kerstin Kessel)
*[[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)  

Revision as of 17:49, 14 April 2010

Home < Documentation < 3.6

This is work in progress

Main GUI


  • Please copy the template linked below, paste it into your page and customize it with your module's information.


  • 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 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

  • The module is feature complete, it does everything that it advertises it can do
  • The module has a test. See here for more information.
  • Module has documentation on the Slicer wiki. Please use the template provided 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. 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 downloadable extensions. The same module creation guidelines apply, but the actual implementation is done outside of the slicer source code repository.
  • Follow Ron's rules for tools
Examples for the Help and

Acknowledgment Panels


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


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)


Informatics Modules




Diffusion MRI


Time Series


Surface Models

Batch processing


Slicer Extensions

Extensions for Downloading


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 here to see a listing of Slicer 3 extensions on NITRC.

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.

  • 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 here


  • Click on the icon to start the extensions wizard

Extensions Wizard

Listing of plug-ins

Available Extensions

  • ABC Marcel Prastawa (prastawa@sci.utah.edu) (a.k.a. Atlas Based Classification) Not yet 3.6. Belongs to segmentation
  • ARCTIC Cedric Mathieu and Clement Vachet (cvachet@email.unc.edu) (a.k.a Automatic Regional Cortical ThICkness) Not yet 3.6. Belongs to wizards
  • BRAINSDemonWarp Hans Johnson (hans-johnson@uiowa.edu) Not yet 3.6. Belongs to registration, robust
  • BRAINSFit Eun Young Kim (eunyoung-kim@uiowa.edu) Not yet 3.6. Belongs to registration robust
  • BRAINSMush Hans Johnson (hans-johnson@uiowa.edu) Not yet 3.6. Belongs to registration robust.
  • CMTK Computational Morphometry Toolkit Torsten Rohlfing (torsten@synapse.sri.com) Not yet 3.6. Belongs to registration robust.
  • EMFiberClusteringModule Mahnaz Maddah (maddah@ge.com) (a.k.a. Quantitative Diffusion Tools) Not yet 3.6. Belongs to tractography
  • FourDAnalysis Junichi Tokuda (tokuda@bwh.harvard.edu) Not yet 3.6
  • HammerRegistration GuorongWu, XiaodongTao, JimMiller, DinggangShen (dgshen@med.unc.edu) Not yet 3.6. Belongs to registration robust.
  • Plastimatch Greg Sharp (gcsharp@partners.org) Not yet 3.6. Belongs to registration robust.
  • SpineSegmentation Sylvain Jaume (sylvain@csail.mit.edu) Not yet 3.6. Belongs to wizards
  • VmtkSlicerModule prerequisite install for all VMTK plug-ins, Daniel Haehn (haehn@bwh.harvard.edu)
  • VMTKCenterlines providing centerline computation of surface models, Daniel Haehn (haehn@bwh.harvard.edu) Not yet 3.6
  • 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
  • VMTKLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution, Daniel Haehn (haehn@bwh.harvard.edu)
  • VMTKVesselEnhancement providing vessel enhancement filters to highlight vascular or tubular structures, Daniel Haehn (haehn@bwh.harvard.edu)

Example Extensions

Non-SPL Supported Compatibility Packages


Slicer 3.6 QA table