Documentation/3.6

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Introduction

3D Slicer is a flexible platform that can be easily extended to enable development of both interactive and batch processing tools for a variety of applications.

3D Slicer provides image registration, processing of DTI (diffusion tractography), an interface to external devices for image guidance support, and GPU-enabled volume rendering, among other capabilities. 3D Slicer has a modular organization that allows the easy addition of new functionality and provides a number of generic features not available in competing tools. Finally, 3D Slicer is distributed under a non-restrictive BSD license.

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 and the following acknowledged here.

  • For information on how to use Slicer 3.6 please go to the training pages.
  • For information on how to obtain Slicer 3.6 please go to the Download Pages.
  • For sample data see here

Main GUI

Modules

Core

Wizards

Informatics Modules

Registration

Segmentation

Quantification

Diffusion MRI

IGT

Time Series

Filtering

Surface Models

Converters

Endoscopy

Slicer Extensions

Extension Status

Introduction

  • Slicer Extensions 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. 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

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

  • 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.
  • 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


Other information

Developer Tools

  • Camera Module (Sebastian Barre)
  • Note: most developer tools are not documented for end users, but contain comments in the source code


Non-SPL Supported Compatibility Packages


QA Table

Slicer 3.6 QA table

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

  • 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

SlicerHelpExample.png
SlicerAcknowledgementExample.png

Please adhere to the naming scheme for the module documentation:

  • [[Modules:MyModuleNameNoSpaces-Documentation-3.6|My Module Name With Spaces] ] (First Last Name)

Documentation Draft notes

Key for flagged modules below:

MissingOrStaleDoc.png: No 3.6 Documentation

MissingOrStaleDocLink.png: Missing or stale link to 3.6 Documentation from Help Panel in software module. If you're not sure how/where to add the link and module description:

  • for command line modules, see other xml files (such as that for the GradientAnisotropicDiffusion Module) for an example of how to add documentation and links to wiki help.
  • for interactive modules, see other modules in Base/GUI for an example.

WeakDoc.png: Weak or Incomplete 3.6 Documentation

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