Documentation/4.0

3D Slicer
Description
Research platform for the analysis and visualization of medical images, including image guided therapy.
Free and extensible open source package.
Multi-platform	Linux, MacOSX, Windows
Version	4.0
License	Contribution and Software License Agreement

4.0 3.6 3.5 3.4 3.2 ALL VERSIONS

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Main GUI Main Application GUI "Hot-keys" and Keyboard Shortcuts Loading or Saving data and listing of supported data formats. Setting up and using stereoscopic viewing Mailing Lists Users mailing list Intended for discussions about the use of Slicer.		Module Categories Core Modules Legacy Utility Wizards Informatics Registration Segmentation Quantification Diffusion IGT Filtering Surface Models Converters Endoscopy Developer Tools		Miscellaneous Visual blog Set of screenshots showing Slicer in action. Training pages Information on how to use Slicer 4.0 FAQ Set of common questions/answers Developers Corner Developers Information Handy Developer Info

Requirements for Modules

• The module is feature complete, i.e. it does everything that it advertises
• The module has a test. See here for more information.
• The module is fully documented. See here for the end-user documentation template.
• The module complies with Rons rules for tool and the style guide lines, including color palette.
• Use the logos in the Logo Gallery

Modules by Category

Core Modules

• Annotations (Nicole Aucoin)
• Colors (Nicole Aucoin)
• Data (Julien Finet)
• DICOM (Steve Pieper)
• Editor (Steve Pieper)
• Models (Nicole Aucoin)
• SceneViews (Nicole Aucoin)
• Transforms (Alex Yarmarkovich)
• View Controllers (Jim Miller)
• Volumes (Steve Pieper)
• Volume Rendering (Julien Finet)
• Welcome to Slicer (Wendy Plesniak)

Legacy

• Converters
  • BSpline to Deformation Field
• Diffusion
  • Denoising
    • Unbiased Non Local Means Filter for DWI
• Filtering
  • MRI Bias Field Correction (Sylvain Jaume)
  • Otsu Threshold (Bill Lorensen)
  • Resample Scalar Valume
• Registration
  • Rigid Registration (Jim Miller)
  • Affine Registration (Daniel Blezek)
• Nonrigid BSpline Registration
  • Nonrigid BSpline Registration
  • Expert Automated Registration
  • Linear Registration
  • Test Grid Transform Registration
  • Robust Multiresolution Affine Registration
• Segmentation
  • Otsu Threshold Segmentation (Bill Lorensen)

Utilities

• Transform MRML Files to NewSegmenter Standard

Wizards

• Change Tracker

Informatics

• Sample Data

Registration

• ACPC Transform (Nicole Aucoin)
• Demon Registration (BRAINS) (Hans Johnson)
• Fiducial Registration (BRAINS) (Casey Goodlett)
• General Registration
• Resample Image (BRAINS) (Hans Johnson)
• Vector Demon Registration

Segmentation

• EMSegment
• EMSegment Command-line
• EMSegment Easy
• Foreground Masking (BRAINS)
• Mesh Contour Segmentation
• Robust Statistics Segmentation (Yi Gao)
• Simple Region Growing

Quantification

• Data Probe
• Demons Registration: Segmentation Based Change Detection (SLOW)
• Intensity Difference Change Detection (FAST)
• Label Statistics (Steve Pieper)
• SUV Computation

Diffusion

• DWI to Full Brain Tractography
• Denoising
  • Joint Rician LMMSE Image Filter
  • Rician LMMSE Image Filter
• Tractography
  • Tractography Display
  • Tractography Fiducial Seeding
  • Tractography Labelmap Seeding
• Utilities
  • Diffusion Tensor Estimation
  • Diffusion Tensor Scalar Measurements
  • Mask from Diffusion Weighted Images
  • Resample DTI Volume

Filtering

• N4ITK Bias Field Correction (Andrey Fedorov)
• CheckerBoard (Bill Lorensen)
• Extract Skeleton
• Histogram Matching (Bill Lorensen)
• Image Label Combine (Alex Yarmarkovich)
• Resample Scalar/Vector/DWI Volume
• Threshold Image (Nicole Aucoin)
• Voting Binary Hole Filling (Jim Miller)
• Resample Tools
  • Resample Volume (Bill Lorensen)
• Arithmetic
  • Add Images (Bill Lorensen)
  • Cast Image (Nicole Aucoin)
  • Mask Image (Nicole Aucoin)
  • Multiply Images (Bill Lorensen)
  • Subtract Images (Bill Lorensen)
• Denoising
  • Gradient Anisotropic Diffusion (Jim Miller)
  • Curvature Anisotropic Diffusion (Bill Lorensen)
  • Gaussian Blur (Stephen Aylward)
  • Median Image Filter (Bill Lorensen)
• Morphology
  • Grayscale Fill Hole (Bill Lorensen)
  • Grayscale Grind Peak (Bill Lorensen)

Surface Models

• Grayscale Model Maker (Bill Lorensen)
• Label Map Smoothing
• Merge Models (Nicole Aucoin)
• Model Maker (Nicole Aucoin)
• PolyData To LabelMap (Nicole Aucoin)
• Probe Volume with Model (Paint)

Converters

• Create Dicom Series (Bill Lorensen)
• Crop Volume
• Dicom to Nrrd Converter (Xiaodong Tao)
• Orient Images (Bill Lorensen)

Endoscopy

• Endoscopy (Steve Pieper)

Developer Tools

• Cameras (Julien Finet)
• Event Broker (Julien Finet)
• Execution Model Tour
• Module Template
• Multiple Models Example
• Performance Tests
• Tractography

Extensions

Introduction

• Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.
• While the Slicer license is suggested for extensions, it is not required. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.
• 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 extensions, please talk directly to the developers of the extensions.
• Information for developers can be found here. See here for the end-user documentation template.
• In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.

Collections

Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.

id	Thumbnail	Name	Short Description	Maturity	Slicer License	Search terms	Contact Information
1		MyCollection	This is a collection of extensions that will do something miraculous with your images			segmentation, level set	my-email at mit.edu

Table Of Extensions

id	Thumbnail	Name	Short Description	Maturity	Slicer License	Search terms	Contact Information
1		MyExtension	This is an extension that will do something wonderful with your data			filter, anisotropic	my-email at gmail.com
2		MyExtension	This is an extension that will do something miraculous with your images			segmentation, level set	my-email at mit.edu

Caption for the table of extensions

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  Distributed under the Slicer License

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  Distributed under a Non Slicer License

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  Work in progress (aka mess)
  Use with care
  Might not work all the time
  Might not be available for all platforms

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  Stable
  Full documentation
  Works as advertised
  Compiles on all supported platforms
  Email support works