Documentation/4.3/Modules

For the latest Slicer documentation, visit the read-the-docs.

Modules by Category

Core Modules

Tractography Module
Browse the image gallery

• Annotations (Nicole Aucoin)
• Colors (Nicole Aucoin)
• Data (Julien Finet)
• DICOM (Steve Pieper)
• Editor (Steve Pieper)
  • WatershedFromMarkers (Bradley Lowekamp)
• Markups (Nicole Aucoin)
• 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)

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 Aided Registration (Yi Gao)

Segmentation

• EMSegment Easy (no atlas) (Kilian Pohl)
• EMSegment (with atlas) (Kilian Pohl)
• Simple Region Growing Segmentation (Jim Miller, Harini Veeraraghavan)
• KSlice Interactive Segmenter (Ivan Kolesov, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )
• Editor (Steve Pieper)
• Specialized
  • EMSegment Command-line (Kilian Pohl)
  • Foreground Masking (BRAINS) (Hans Johnson)
  • Robust Statistics Segmenter (Yi Gao)
  • Left Atrial Scar Segmenter (Liangjia Zhu)
  • Left Atrium Segmenter (Liangjia Zhu)
  • Fast GrowCut Effect (Liangjia Zhu)

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 Interactive Seeding (Alex Yarmarkovich)
  • Tractography Label Map Seeding (Demian Wasserman)
  • UKF Tractography
• Utilities
  • DWI To DTI Estimation (Demian Wasserman)
  • Diffusion Tensor Scalar Measurements (Demian Wasserman)
  • Diffusion Weighted Volume Masking (Demian Wasserman)
  • FiberBundleLabelSelect (Alex Yarmarkovich)
  • Resample DTI Volume (Demian Wasserman)
• Data Conversion
  • DTIImport (Sonia Pujol)
  • DTIExport (Sonia Pujol)
  • Fiber Bundle to Label Map (Steve Pieper)

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 Scalar Volume (Nicole Aucoin)
• Voting Binary Hole Filling Image Filter (Jim Miller)
• Simple Filters (Bradley Lowekamp)
• 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)
• SurfaceToolbox (Luca Antiga)

Converters

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

Endoscopy

• Endoscopy (Steve Pieper)

Work in Progress

• MultiVolume Support
  • MultiVolume Importer (Andrey Fedorov)
  • MultiVolume Explorer (Andrey Fedorov)
• Data Store (Charles Marion)

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)