Documentation/4.0

4.0 3.6 3.5 3.4 3.2 ALL VERSIONS

Table of Content

Slicer Application Main Application GUI Mouse Buttons, "Hot-keys" and Keyboard Shortcuts (Wendy Plesniak) Computer configurations Loading or Saving data and listing of supported data formats. (Julien Finet) Setting up and using stereoscopic viewing Mailing Lists Mailing list for users Search in archives on nabble.com Mailing list for developers Search in archives on nabble.com		Module Categories Core Modules Wizards Informatics Registration Segmentation Quantification Diffusion IGT Filtering Surface Models Converters Endoscopy Developer Tools Legacy		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 Release Notes Platform specific issues and considerations Developers Corner Information for Software Developers Where to find the source code, how to compile ...

General Information

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

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

• ChangeTracker (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)
  • Reformat (Michael Jeulin-Lagarrigue)

Segmentation

• EMSegment Easy (no atlas) (Kilian Pohl)
• EMSegment (with atlas) (Kilian Pohl)
• Simple Region Growing Segmentation (Jim Miller, Harini Veeraraghavan)
• 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)
• Label Statistics (Steve Pieper)
• PET Standard Uptake Value Computation (Nicole Aucoin)
• Change quantification
  • Intensity Difference Metric (Andrey Fedorov)

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
  • DWI To DTI Estimation (Demian Wasserman)
  • Diffusion Tensor Scalar Measurements (Demian Wasserman)
  • Diffusion Weighted Volume Masking (Demian Wasserman)
  • Resample DTI Volume (Demian Wasserman)

IGT

• OpenIGTLink IF (Junichi Tokuda)

Filtering

• N4ITK Bias Field Correction (Andrey Fedorov)
• CheckerBoard Filter (Jim Miller)
• Extract Skeleton (Jim Miller)
• 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 Scalar Volume (Jim Miller)
• Arithmetic
  • Add Scalar Volumes (Jim Miller)
  • Cast Scalar Volume (Nicole Aucoin)
  • Mask Scalar Volume (Nicole Aucoin)
  • Multiply Scalar Volumes (Jim Miller)
  • Subtract Scalar Volumes (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 (Jim Miller)
• Label Map Smoothing
• Merge Models (Nicole Aucoin)
• Model Maker (Nicole Aucoin)
• Model To LabelMap (Nicole Aucoin)
• Probe Volume with Model (Paint) (Lauren O'Donnell)

Converters

• Create Dicom Series (Jim Miller)
• Crop Volume (Andrey Fedorov)
• Dicom to Nrrd Converter (Jim Miller)
• Orient Scalar Volume (Jim Miller)

Endoscopy

• Endoscopy (Steve Pieper)

Developer Tools

• Cameras (Julien Finet)
• Event Broker (Julien Finet)
• Execution Model Tour (JC Fillion-Robin)
• 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 Image Filter (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)

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

• 

  Distributed under the Slicer License

• 

  Distributed under a Non Slicer License

• 

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

• 

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