Documentation/3.5

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Home < Documentation < 3.5

Modules

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

Slicer3:Module_Documentation-3.5_Template

  • See below 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-3.5|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 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 Acknowledgment 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.
    • 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.)
 Examples for the Help and

Acknowledgment Panels

SlicerHelpExample.png
SlicerAcknowledgementExample.png

List of Modules new to 3.5

List of pre-existing Modules

Core

Specialized Modules

Please adhere to the naming scheme for the module documentation:

  • [ [Modules:MyModuleNameNoSpaces-Documentation-3.4|My Module Name With Spaces] ] (First Last Name)

Wizards

Informatics Modules

Registration

  • Overview:
    • The Register Images module is an integrated solution to all your registration needs, if you want to have a resampled volume as output. It provides access to rigid, affine and b-spline itk technologies.
    • The Transforms Module allows to manually align two volumes. This can be used for initial alignment.
    • Linear, affine and Deformable B-Spline modules can be used stand-alone or one after the other. They can accept transformation matrices as the start pose and produce either transforms or resampled volumes as output.
    • Transformation matrices derived from these modules can be used as input for resampling other volumes (including DTI) using the Resample Volume 2 module.
  • Register Images (Stephen Aylward)
  • Transforms Module (Alex Yarmarkovich)
  • Linear Registration (Daniel Blezek)
  • Affine Registration (Daniel Blezek)
  • Deformable B-Spline Registration (Bill Lorensen)
  • ACPC Transform (Nicole Aucoin)

Segmentation

Statistics

Diffusion

DWI

DTI

Tractography

IGT

Filtering

Surface Models

  • Modelmaker (Nicole Aucoin)
  • Grayscale Model Maker (Bill Lorensen)

Batch processing

Converters

Slicer Extensions

  • 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.
  • 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.
  • Extensions are compiled as part of the nightly build. In order to set this up, please contact the Slicer team.

Installation

Use the Slicer Extension wizard to install extensions. Click on the icon to start the wizard

VMTK

  • There are 4 vmtk modules. You need to install the library module to run any of the other three.
  • VMTKEasyLevelSetSegmentation - providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface
  • VMTKLevelSetSegmentation - providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms
  • VMTKVesselEnhancement - providing vessel enhancement filters to highlight vasculature or tubular structures

EM DTI Clustering

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