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 Wizards Informatics Registration Segmentation Quantification Diffusion IGT Filtering Surface Models Converters Endoscopy Developer Tools Legacy Utility		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. Template and How-to for the end user documentation.
• 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)

Wizards

• Change Tracker (Andrey Fedorov)

Informatics

• Sample Data (Steve Pieper)

Registration

• General Brainsfit Registration (Hans Johnson)
• Resample Image (BRAINS) (Hans Johnson)
• Specialized
  • ACPC Transform (Nicole Aucoin)
  • Demon Registration (BRAINS) (Hans Johnson)
  • Fiducial Registration (BRAINS) (Stephen Aylward)
  • Vector Demon Registration (Hans Johnson)

Segmentation

• EMSegment Easy (no atlas) (Kilian Pohl)
• EMSegment (with atlas) (Kilian Pohl)
• Simple Region Growing (Jim Miller)
• Specialized
  • EMSegment Command-line (Kilian Pohl)
  • Foreground Masking (BRAINS) (Hans Johnson)
  • Mesh Contour Segmentation (Allen Tannenbaum)
  • Robust Statistics Segmentation (Yi Gao)

Quantification

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

Diffusion

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

Filtering

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

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 (Jim Miller)
• Crop Volume
• Dicom to Nrrd Converter (Jim Miller)
• Orient Images (Jim Miller)

Endoscopy

• Endoscopy (Steve Pieper)

Developer Tools

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

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 Volume
• 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

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