Documentation/4.1

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Table of Content

Slicer Application Main Application GUI Mouse Buttons, "Hot-keys" and Keyboard Shortcuts Computer Configurations Loading or Saving data and listing of supported data formats. (Julien Finet) Slicer Lookup Tables 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 Work in Progress Developer Tools Legacy		Miscellaneous Visual blog Set of screenshots showing Slicer in action. Training pages Information on how to use Slicer 4.1 FAQ Set of common questions/answers Release Notes Platform specific issues and considerations Announcements the announcement associated with Slicer 4.1 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 4.1 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

• Introduction to Registration (Dominik Meier)
• General Brainsfit Registration (Hans Johnson)
• Resample Image (BRAINS) (Hans Johnson)
• Specialized
  • ACPC Transform (Nicole Aucoin)
  • Demon Registration (BRAINS) (Hans Johnson)
  • Fiducial Registration (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)
  • Robust Statistics Segmenter (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
  • DWI Joint Rician LMMSE Image Filter (Demian Wasserman)
  • DWI Rician LMMSE Filter (Demian Wasserman)
• Tractography
  • Tractography Display (Demian Wasserman)
  • Tractography Fiducial Seeding (Demian Wasserman)
  • Tractography Label Map 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)
• Data Conversion
  • DTIImport (Sonia Pujol)
  • DTIExport (Sonia Pujol)

IGT

• OpenIGTLink IF (Junichi Tokuda)
• Volume Reslice Driver (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 Scalar Volume (Nicole Aucoin)
• Voting Binary Hole Filling Image Filter (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 Image Filter (Stephen Aylward)
  • Median Image Filter (Jim Miller)
• Morphology
  • Grayscale Fill Hole Image Filter (Jim Miller)
  • Grayscale Grind Peak Image Filter (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 (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)

Work in Progress

• MultiVolume Support
  • MultiVolume Importer (Andrey Fedorov)
  • MultiVolume Explorer (Andrey Fedorov)

Developer Tools

• Cameras (Julien Finet)
• Event Broker (Julien Finet)
• Execution Model Tour (JC Fillion-Robin)
• Module Template (JC Fillion-Robin)
• Performance Tests
• Tractography

Legacy

• Converters
  • BSpline To Deformation Field
• Diffusion
  • Denoising
    • DWI Unbiased Non Local Means Filter
• Filtering
  • MRI Bias Field Correction (Sylvain Jaume)
  • Otsu Threshold Image Filter (Bill Lorensen)
  • Resample Scalar Volume (Jim Miller)
• Registration
  • Rigid Registration (Jim Miller)
  • Affine Registration (Daniel Blezek)
  • BSpline Deformable Registration
  • Expert Automated Registration
  • Linear Registration
  • MultiResolution Affine Registration (Casey Goodlett)
• Segmentation
  • Otsu Threshold Segmentation (Bill Lorensen)

Legacy

• Converters
  • BSpline To Deformation Field
• Diffusion
  • Denoising
    • DWI Unbiased Non Local Means Filter
• Filtering
  • MRI Bias Field Correction (Sylvain Jaume)
  • Otsu Threshold Image Filter (Bill Lorensen)
  • Resample Scalar Volume (Jim Miller)
• Registration
  • Rigid Registration (Jim Miller)
  • Affine Registration (Daniel Blezek)
  • BSpline Deformable Registration
  • Expert Automated Registration
  • Linear Registration
  • MultiResolution Affine Registration (Casey Goodlett)
• Segmentation
  • Otsu Threshold Segmentation (Bill Lorensen)

Extensions

Introduction

Extensions which can be added to the basic Slicer package in order to add functionality. The slicer community maintains a website to support finding, downloading and installing Extensions for 3D Slicer 4. Access to this website is integral to Slicer 4 and facilitated by the Extensions Manager functionality built into the distributed program. Please see here for information for software developers on how to add your extension to this website.

The download site is referred to as the Slicer Extensions Catalog. The Catalog classifies extensions into three levels of compliance:

• Category 1: Fully compliant Slicer Extensions: Slicer license, open source, maintained.
• Category 2: open source, contact exists.
• Category 3: all other extensions (work in progress, beta, closed source etc).

See here for more information about extension types and policies.

Cat 2

• SkullStripper (Xiaodong Tao)
• CARMA (Alan Morris)

Cat 3

• Plastimatch (Greg Sharp)
  • Plastimatch Automatic deformable image registration (Greg Sharp)
  • Plastimatch DICOM-RT import (Greg Sharp)
  • Plastimatch DICOM-RT export (Greg Sharp)
  • Plastimatch Dose Comparison (Greg Sharp)
  • Plastimatch Dose Volume Histogram (Greg Sharp)
  • Plastimatch LANDWARP Landmark (Greg Sharp)
  • Plastimatch Synthetic Image Generation (Greg Sharp)
  • Plastimatch Threshold in a box (Greg Sharp)
  • Plastimatch XFORMWARP (Greg Sharp)