Documentation/4.6

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

Nightly 4.10 4.8 4.6 4.5 4.4 4.3 4.2 4.1 4.0 3.6 3.5 3.4 3.2 ALL VERSIONS

Where to start ? Getting started Quick overview about Slicer Training pages Information on how to use Slicer 4.6 FAQ Set of common questions/answers Search users mailing list / Sign-up How to Report a problem / Create a feature request  NEW Slicer Application Installation Main Application GUI Settings Extensions Manager Mouse Buttons, "Hot-keys" and Keyboard Shortcuts Recommended Computer Configurations Loading or Saving data and listing of supported data formats. Slicer Lookup Tables Setting up and using stereoscopic viewing QtTesting - Easy way to record and play macros		Modules and Extensions Modules by category Modules by name Modules by contributing organization Modules by contributing individual Modules by type Modules by extension Extensions by category Extensions by name Extensions by contributing organization Extensions by contributing individual List of extensions known to be broken		Developers Corner Information for Software Developers  UPDATED Source code, contribute patch, develop modules Discussion Forum Miscellaneous Documentation guidelines Slicer user documentation principle and guidelines Visual blog Set of screenshots showing Slicer in action. Release Notes Platform specific issues and considerations Announcements & Acknowledgments Registration Library Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself. Documentation in other languages Español

Modules by category

36 categories:

• Cardiac
• Cardiac MRI Toolkit
• Chest Imaging Platform
  • Modules
  • Toolkit
    • Particles
    • Processing
    • Quantification
    • Registration
    • Segmentation
    • Utils
• CIP
• Converters
• Developer Tools
  • DICOM Plugins
  • Editor Extensions
  • Matlab
• Diffusion
  • Diffusion Data Conversion
  • Diffusion Tensor Images
  • Diffusion Weighted Images
  • Process
  • Quantify
  • Tractography
    • Region-based
  • Utilities
• Editor Effects
• Editor Effect
• Endoscopy
• Examples
• Exporter
• Filter
• Filtering
  • Arithmetic
  • Denoising
  • Morphology
• IGT
• Informatics
  • Converters
• Legacy
  • Converters
  • Filtering
  • Registration
  • Work in Progress
    • Diffusion Tensor
      • Test
• Margin Calculator
• Mesh Generation
• Mesh Generation
• Microscopy
• Multi Volume Support
• Plastimatch
  • Registration
  • Utilities
• Quantification
  • Change Quantification
• Radiotherapy
• Registration
  • CMF Registration
    • Voxelbase Registration
  • Label Registration
  • Specialized
• Segmentation
  • Specialized
• Sequences
• Shape Analysis
• Slicelets
• Surface Models
• Test Cases
• Testing
  • IGT Tests
  • Slicer RT Tests
  • Test Cases
• Utilities
  • BRAINS
• Vascular Modeling Toolkit
• Wizards

Cardiac

• Philips4d Us Dicom Patcher (scripted, bundled in Slicer Heart extension)
• Valve View (scripted, bundled in Slicer Heart extension)

Cardiac MRI Toolkit

• CMRToolkit PVAntrum Cut (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Boolean REMOVEFilter (cli, bundled in Cardiac MRI Toolkit extension)
• LASegmentation Workflow (scripted, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Registration BRAINSFit (scripted, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Automatic Left Atrial Scar (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Connected Threshold Filter (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Wizard (scripted, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Isolated Connected Filter (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Inhomogeneity Correction (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Axial Dilate (cli, bundled in Cardiac MRI Toolkit extension)
• Scar Visualization (scripted, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Registration (scripted, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit LASegmentation Graph Cuts (cli, bundled in Cardiac MRI Toolkit extension)

Chest Imaging Platform

• Interactive Lobe Segmentation (scripted, bundled in Chest Imaging Platform extension)
• Airway Inspector (loadable, bundled in Chest Imaging Platform extension)

Modules

• CIP MIPViewer (scripted, bundled in Chest Imaging Platform extension)
• CIP Body Composition (scripted, bundled in Chest Imaging Platform extension)
• CIP Trachea Stent Planning (scripted, bundled in Chest Imaging Platform extension)
• CIP Lesion Model (scripted, bundled in Chest Imaging Platform extension)
• CIP PAARatio (scripted, bundled in Chest Imaging Platform extension)
• CIP Parenchyma Subtype Training (scripted, bundled in Chest Imaging Platform extension)

Toolkit

Particles

• Extract Particles From Chest Region Chest Type (cli, bundled in Chest Imaging Platform extension)
• Filter Vessel Particle Data (cli, bundled in Chest Imaging Platform extension)
• Remove Particles From Particles Data Set (cli, bundled in Chest Imaging Platform extension)
• Merge Particle Data Sets (cli, bundled in Chest Imaging Platform extension)
• Perturb Particles (cli, bundled in Chest Imaging Platform extension)
• Filter Airway Particle Data (cli, bundled in Chest Imaging Platform extension)
• Fit Lobe Surface Models To Particle Data (cli, bundled in Chest Imaging Platform extension)
• Classify Fissure Particles (cli, bundled in Chest Imaging Platform extension)
• Generate Stenciled Label Map From Particles (cli, bundled in Chest Imaging Platform extension)
• Filter Fissure Particle Data (cli, bundled in Chest Imaging Platform extension)

Processing

• Resample Label Map (cli, bundled in Chest Imaging Platform extension)
• Rescale Label Map (cli, bundled in Chest Imaging Platform extension)
• Generate Median Filtered Image (cli, bundled in Chest Imaging Platform extension)
• Label Map From Region And Type Points (cli, bundled in Chest Imaging Platform extension)
• Crop Lung (cli, bundled in Chest Imaging Platform extension)
• Generate NLMFiltered Image (cli, bundled in Chest Imaging Platform extension)
• Remove Chest Type From Label Map Using Particles (cli, bundled in Chest Imaging Platform extension)
• Generate Atlas Convex Hull (cli, bundled in Chest Imaging Platform extension)
• Compute Fissure Feature Vectors (cli, bundled in Chest Imaging Platform extension)
• Generate Lobe Surface Models (cli, bundled in Chest Imaging Platform extension)
• Filter Connected Components (cli, bundled in Chest Imaging Platform extension)
• Extract Chest Label Map (cli, bundled in Chest Imaging Platform extension)
• Perform Morphological (cli, bundled in Chest Imaging Platform extension)
• Extract Fissure Boundary From Lobe Map (cli, bundled in Chest Imaging Platform extension)
• Enhance Fissures In Image (cli, bundled in Chest Imaging Platform extension)
• Remap Label Map (cli, bundled in Chest Imaging Platform extension)
• Generate Distance Map From Label Map (cli, bundled in Chest Imaging Platform extension)
• Resample CT (cli, bundled in Chest Imaging Platform extension)
• Compute Feature Strength (cli, bundled in Chest Imaging Platform extension)
• Compute Distance Map (cli, bundled in Chest Imaging Platform extension)
• Quality Control (cli, bundled in Chest Imaging Platform extension)
• Generate Image Sub Volumes (cli, bundled in Chest Imaging Platform extension)

Quantification

• Evaluate Lung Lobe Segmentation Results (cli, bundled in Chest Imaging Platform extension)
• Get Transformation Kappa (cli, bundled in Chest Imaging Platform extension)
• Read Write Image Data (cli, bundled in Chest Imaging Platform extension)
• Compute Intensity Statistics (cli, bundled in Chest Imaging Platform extension)
• Compute Cross Sectional Area (cli, bundled in Chest Imaging Platform extension)
• Label Particles By Chest Region Chest Type (cli, bundled in Chest Imaging Platform extension)
• Get Transformation Similarity Metric (cli, bundled in Chest Imaging Platform extension)
• Generate Region Histograms And Parenchyma Phenotypes (cli, bundled in Chest Imaging Platform extension)
• Get Transformation Kappa2D (cli, bundled in Chest Imaging Platform extension)

Registration

• Register Lung Atlas (cli, bundled in Chest Imaging Platform extension)
• Register Label Maps (cli, bundled in Chest Imaging Platform extension)
• Register CT (cli, bundled in Chest Imaging Platform extension)

Segmentation

• Generate Otsu Lung Cast (cli, bundled in Chest Imaging Platform extension)
• Segment Lung Lobes (cli, bundled in Chest Imaging Platform extension)
• Generate Partial Lung Label Map (cli, bundled in Chest Imaging Platform extension)
• Split Left Lung Right Lung (cli, bundled in Chest Imaging Platform extension)
• Generate Binary Thinning3D (cli, bundled in Chest Imaging Platform extension)
• Generate Lesion Segmentation (cli, bundled in Chest Imaging Platform extension)

Utils

• Convert Dicom (cli, bundled in Chest Imaging Platform extension)
• Region Type Locations To ROIVolume (cli, bundled in Chest Imaging Platform extension)
• Read VTKWrite NRRDs (cli, bundled in Chest Imaging Platform extension)
• Generate Overlay Images (cli, bundled in Chest Imaging Platform extension)
• Execute System Command (cli, bundled in Chest Imaging Platform extension)
• Get Structures In Label Map (cli, bundled in Chest Imaging Platform extension)
• Find Patch Match (cli, bundled in Chest Imaging Platform extension)
• Convert Chest Region Chest Type To Label Map Value (cli, bundled in Chest Imaging Platform extension)
• Mask Out Label Map Structures (cli, bundled in Chest Imaging Platform extension)
• Read NRRDs Write VTK (cli, bundled in Chest Imaging Platform extension)
• Convert Label Map Value To Chest Region Chest Type (cli, bundled in Chest Imaging Platform extension)
• Read Write Region And Type Points (cli, bundled in Chest Imaging Platform extension)
• Merge Chest Label Maps (cli, bundled in Chest Imaging Platform extension)
• Read Vida Write CIP (cli, bundled in Chest Imaging Platform extension)
• Read Dicom Write Tags (cli, bundled in Chest Imaging Platform extension)
• Transfer Region And Type Indices To From Points (cli, bundled in Chest Imaging Platform extension)

CIP

• CIP Common (scripted, bundled in Chest Imaging Platform extension)

Converters

• Quad Edge Surface Mesher (cli, bundled in Slicer Prostate extension)
• Crop Volume (loadable, built-in)
• Orient Scalar Volume (cli, built-in)
• Convert VTK (cli, bundled in UKFTractography extension)
• Vector To Scalar Volume (scripted, built-in)
• Create DICOMSeries (cli, built-in)
• Particles Display (loadable, bundled in Chest Imaging Platform extension)
• Region Type (loadable, bundled in Chest Imaging Platform extension)

Developer Tools

• Cameras (loadable, built-in)
• Execution Model Tour (cli, built-in)
• Node Modified Statistics (scripted, bundled in Debugging Tools extension)
• Py Dev Remote Debug (scripted, bundled in Debugging Tools extension)
• Extension Wizard (scripted, built-in)
• Image Maker (cli, bundled in Image Maker extension)
• Extension Stats (scripted, bundled in Developer Tools For Extensions extension)
• Developer Tools For Extensions (scripted, bundled in Developer Tools For Extensions extension)
• Event Broker
• Double Arrays (loadable, built-in)

DICOM Plugins

• Dicom Ultrasound Plugin
• DICOMSegmentation Plugin
• DICOMSlicer Data Bundle Plugin
• DICOMPETSUVPlugin
• DICOMDiffusion Volume Plugin
• DICOMLongitudinal PETCTPlugin
• Dicom Sro Import Plugin
• DICOMScalar Volume Plugin
• DICOMRWVMPlugin
• Dicom Rt Import Export Plugin
• Multi Volume Importer Plugin

Editor Extensions

• Fast Grow Cut Effect (scripted, bundled in Fast Grow Cut Effect extension)
• Carrera Slice Effect (scripted, bundled in Carrera Slice extension)
• PETTumor Segmentation Effect (scripted, bundled in PETTumor Segmentation extension)
• Binary Watershed Effect (scripted, bundled in IASEM extension)
• Double Threshold Effect (scripted, bundled in IASEM extension)

Matlab

• Matlab Module Generator (loadable, bundled in Matlab Bridge extension)
• Matlab Commander (cli, bundled in Matlab Bridge extension)

Diffusion

Diffusion Data Conversion

• DWIConverter (cli, built-in)

Diffusion Tensor Images

• Resample DTIlog Euclidean (cli, bundled in Resample DTIlog Euclidean extension)

Diffusion Weighted Images

• BRAINSDWICleanup (cli, built-in)
• Finsler Backtracing (cli, bundled in Finsler Tractography extension)
• Finsler Tractography (cli, bundled in Finsler Tractography extension)

Process

• Diffusion Brain Masking (cli, built-in)
• Diffusion Tensor Estimation (cli, built-in)

Quantify

• Diffusion Tensor Scalar Maps (cli, built-in)
• Tractography Measurements (cli, built-in)

Tractography

• Tractography Display (loadable, built-in)
• Tractography Seeding (loadable, built-in)
• UKFTractography (cli, bundled in UKFTractography extension)

Region-based

• Tractography ROI Seeding (cli, built-in)
• Tractography ROI Selection (cli, built-in)

Utilities

• Tractography DICOM Load (cli, built-in)
• Tractography DICOM Save (cli, built-in)
• DWI to Full Brain Tractography (cli, built-in)
• Resample DTIVolume (cli, built-in)
• Resample Scalar/Vector/DWI Volume (cli, built-in)
• Tractography to Mask Image (scripted, built-in)

Editor Effects

• Window Level Effect (scripted, bundled in Window Level Effect extension)

EditorEffect

• PETTumor Segmentation (loadable, bundled in PETTumor Segmentation extension)

Endoscopy

• Endoscopy (scripted, built-in)

Examples

• Fast Grow Cut (loadable, bundled in Fast Grow Cut Effect extension)
• Fast Grow Cut Segmenter (loadable, bundled in Carrera Slice extension)
• Carrera Slice (loadable, bundled in Carrera Slice extension)
• Graph Cut Interactive Segmenter (loadable, bundled in Graph Cut Segment extension)

Exporter

• Slicer To Kiwi Exporter (scripted, bundled in Slicer To Kiwi Exporter extension)

Filter

• Island Removal (cli, built-in)

Filtering

• Segmentation Smoothing (cli, bundled in Slicer Prostate extension)
• N4ITKBias Field Correction (cli, built-in)
• Image Label Combine (cli, built-in)
• Voting Binary Hole Filling Image Filter (cli, built-in)
• Checker Board Filter (cli, built-in)
• Extract Skeleton (cli, built-in)
• Simple Filters (scripted, built-in)
• Threshold Scalar Volume (cli, built-in)
• Histogram Matching (cli, built-in)

Arithmetic

• Multiply Scalar Volumes (cli, built-in)
• Add Scalar Volumes (cli, built-in)
• Mask Scalar Volume (cli, built-in)
• Subtract Scalar Volumes (cli, built-in)
• Cast Scalar Volume (cli, built-in)

Denoising

• Curvature Anisotropic Diffusion (cli, built-in)
• Gradient Anisotropic Diffusion (cli, built-in)
• Median Image Filter (cli, built-in)
• Gaussian Blur Image Filter (cli, built-in)

Morphology

• Grayscale Fill Hole Image Filter (cli, built-in)
• Grayscale Grind Peak Image Filter (cli, built-in)

IGT

• Viewpoint (scripted, bundled in Lump Nav extension)
• Collect Fiducials (loadable, bundled in Slicer IGT extension)
• Lump Nav (scripted, bundled in Lump Nav extension)
• Transform Fusion (loadable, bundled in Slicer IGT extension)
• Gyro Guide (scripted, bundled in Gyro Guide extension)
• Create Models (loadable, bundled in Slicer IGT extension)
• Needle Finder (scripted, bundled in Needle Finder extension)
• Tracker Stabilizer (loadable, bundled in Tracker Stabilizer extension)
• Path Explorer (loadable, bundled in Slicer IGT extension)
• Ultrasound Snapshots (loadable, bundled in Slicer IGT extension)
• Breach Warning Light (scripted, bundled in Lump Nav extension)
• Breach Warning (loadable, bundled in Slicer IGT extension)
• Model Registration (scripted, bundled in Slicer IGT extension)
• Pivot Calibration (loadable, bundled in Slicer IGT extension)
• Volume Reslice Driver (loadable, bundled in Slicer IGT extension)
• Fiducial Registration Wizard (loadable, bundled in Slicer IGT extension)
• Open IGTLink Remote (loadable, bundled in Slicer IGT extension)
• Watchdog (loadable, bundled in Slicer IGT extension)
• Corner Annotation (scripted, bundled in Corner Annotation extension)
• Open IGTLink IF (loadable, built-in)
• i Gyne (scripted, bundled in i Gyne extension)
• Plus Remote (scripted, bundled in Slicer IGT extension)
• Fiducials To Model Registration (scripted, bundled in Slicer IGT extension)
• Markups To Model (loadable, bundled in Slicer IGT extension)

Informatics

• mp Review Preprocessor (scripted, bundled in mp Review extension)
• Tables (loadable, built-in)
• SEG2NRRD (cli, bundled in Reporting extension)
• TCIABrowser (scripted, bundled in TCIABrowser extension)
• mp Review (scripted, bundled in mp Review extension)
• Data (loadable, built-in)
• Units (loadable, built-in)
• DICOM (scripted, built-in)
• Sample Data (scripted, built-in)
• Colors (loadable, built-in)
• Curve Maker (scripted, bundled in Curve Maker extension)
• Annotations (loadable, built-in)
• Markups (loadable, built-in)
• Subject Hierarchy (loadable, built-in)

Converters

• Encode SEG (cli, bundled in Reporting extension)

Legacy

Converters

• BSpline To Deformation Field (cli, built-in)

Filtering

• Otsu Threshold Image Filter (cli, built-in)
• Resample Scalar Volume (cli, built-in)

Registration

• Test Grid Transform Registration (cli, built-in)
• Expert Automated Registration (cli, built-in)

Work in Progress

Diffusion Tensor

Test

• Diffusion Tensor Test (cli, built-in)

Margin Calculator

• Margin Calculator (scripted, bundled in Margin Calculator extension)
• Dose Morphology (loadable, bundled in Margin Calculator extension)
• Dose Population Histogram (loadable, bundled in Margin Calculator extension)
• Motion Simulator (loadable, bundled in Margin Calculator extension)
• Synthetic RTDose (scripted, bundled in Margin Calculator extension)
• Motion Simulator Double Array (loadable, bundled in Margin Calculator extension)

Mesh Generation

• Cleaver CLI (cli, bundled in Cleaver Extension extension)

MeshGeneration

• Body Centric Cubic Mesh (cli, bundled in CBC 3D I2MConversion extension)
• Mesh Compression (cli, bundled in CBC 3D I2MConversion extension)

Microscopy

• IASEMImport Series (cli, bundled in IASEM extension)
• IASEMImport (cli, bundled in IASEM extension)
• Bin Shrink (cli, bundled in IASEM extension)
• Label Object Statistics (scripted, bundled in IASEM extension)
• Spacing Aware Curvature Diffusion (cli, bundled in IASEM extension)

MultiVolume Support

• Multi Volume Importer (scripted, built-in)
• Multi Volume Explorer (loadable, built-in)

Plastimatch

• Dicom Sro Export (scripted, bundled in Slicer RT extension)
• Plm Register (scripted, bundled in Slicer RT extension)

Registration

• plastimatch slicer bspline (cli, bundled in Slicer RT extension)
• plastimatch slicer landwarp (cli, bundled in Slicer RT extension)

Utilities

• Plastimatch Py (loadable, bundled in Slicer RT extension)

Quantification

• DSCMRIAnalysis (cli, bundled in DSCMRIAnalysis extension)
• PETIndi C (scripted, bundled in PET-Indi C extension)
• Q3DC (scripted, bundled in Q3DC extension)
• Heterogeneity CAD (scripted, bundled in Open CAD extension)
• Quantitative Indices CLI (cli, bundled in PET-Indi C extension)
• PETStandard Uptake Value Computation (cli, built-in)
• SUVFactor Calculator (cli, bundled in PETDICOMExtension extension)
• Spinal Curvature Measurement (scripted, bundled in Scoliosis extension)
• Quantitative Indices Tool (scripted, bundled in PET-Indi C extension)
• Label Statistics (scripted, built-in)
• DWModeling (cli, bundled in Slicer Prostate extension)
• BRAINSLabel Stats (cli, built-in)
• Pk Modeling (cli, bundled in Pk Modeling extension)
• PETSUVImage Maker (cli, bundled in Longitudinal PETCT extension)
• Data Probe (scripted, built-in)
• T1Mapping (cli, bundled in T1Mapping extension)
• Angle Planes (scripted, bundled in Angle Planes Extension extension)
• d Pet Brain Quantification (scripted, bundled in Pet Spect Analysis extension)
• Pick And Paint (scripted, bundled in Pick And Paint Extension extension)
• Dice Computation (loadable, bundled in Dice Computation extension)

ChangeQuantification

• Intensity Difference Metric (cli, bundled in Change Tracker extension)

Radiotherapy

• Beams (loadable, bundled in Slicer RT extension)
• Dvh Comparison (scripted, bundled in Slicer RT extension)
• Isodose (loadable, bundled in Slicer RT extension)
• Dose Volume Histogram (loadable, bundled in Slicer RT extension)
• Dicom Rt Import Export (loadable, bundled in Slicer RT extension)
• Dose Accumulation (loadable, bundled in Slicer RT extension)
• Segment Comparison (loadable, bundled in Slicer RT extension)
• Planar Image (loadable, bundled in Slicer RT extension)
• Segment Morphology (loadable, bundled in Slicer RT extension)
• Dose Comparison (loadable, bundled in Slicer RT extension)
• Dicom Sro Import (loadable, bundled in Slicer RT extension)

Registration

• Transforms (loadable, built-in)
• BRAINSResize (cli, built-in)
• Perform Metric Test (cli, built-in)
• Landmark Registration (scripted, built-in)
• PBNRR (cli, bundled in PBNRR extension)
• BRAINSResample (cli, built-in)
• BRAINSFit (cli, built-in)

CMF Registration

• Apply Matrix (cli, bundled in CMFreg extension)
• Label Addition (cli, bundled in CMFreg extension)
• Downsize (cli, bundled in CMFreg extension)
• Surface Registration (scripted, bundled in CMFreg extension)
• Label Extraction (cli, bundled in CMFreg extension)

Voxelbase Registration

• Non Growing (cli, bundled in CMFreg extension)
• Growing (cli, bundled in CMFreg extension)
• Mask Creation (cli, bundled in CMFreg extension)

Label Registration

• Distance Map Based Registration (scripted, bundled in Slicer Prostate extension)

Specialized

• ACPCTransform (cli, built-in)
• Fiducial Registration (cli, built-in)
• BRAINSDemon Warp (cli, built-in)
• Reformat (loadable, built-in)
• VBRAINSDemon Warp (cli, built-in)

Segmentation

• EMSegment Quick (loadable, built-in)
• Volume Clip With Model (scripted, bundled in Volume Clip extension)
• ABC (cli, bundled in ABC extension)
• Airway Segmentation CLI (cli, bundled in Airway Segmentation extension)
• LAScar Segmenter (cli, bundled in LAScar Segmenter extension)
• Segment Editor (scripted, bundled in Slicer RT extension)
• Airway Segmentation (scripted, bundled in Airway Segmentation extension)
• Skull Stripper (cli, bundled in Skull Stripper extension)
• Volume Clip With Roi (scripted, bundled in Volume Clip extension)
• Segment CAD (scripted, bundled in Open CAD extension)
• Swiss Skull Stripper (cli, bundled in Swiss Skull Stripper extension)
• Wasp (scripted, bundled in Wasp extension)
• Editor (scripted, built-in)
• Simple Region Growing Segmentation (cli, built-in)
• EMSegment (loadable, built-in)
• Intensity Segmenter (cli, bundled in Intensity Segmenter extension)

Specialized

• BRAINSROIAuto (cli, built-in)
• Robust Statistics Segmenter (cli, built-in)
• EMSegment Command Line (cli, built-in)

Sequences

• Sequences (loadable, bundled in Sequences extension)
• Sequence Browser (loadable, bundled in Sequences extension)
• Metafile Importer (loadable, bundled in Sequences extension)

Shape Analysis

• Model To Model Distance (cli, bundled in Model To Model Distance extension)

Slicelets

• Gel Dosimetry Analysis (scripted, bundled in Gel Dosimetry Analysis extension)
• Gel Dosimetry Analysis Algo (loadable, bundled in Gel Dosimetry Analysis extension)

Surface Models

• Surface Toolbox (scripted, built-in)
• Grayscale Model Maker (cli, built-in)
• Model Maker (cli, built-in)
• Model To Label Map (cli, built-in)
• Merge Models (cli, built-in)
• Easy Clip (scripted, bundled in Easy Clip extension)
• Label Map Smoothing (cli, built-in)
• Mesh To Label Map (cli, bundled in Mesh To Label Map extension)
• Probe Volume With Model (cli, built-in)

TestCases

• SEGExporter Self Test

Testing

• CLI4Test
• Threshold Threading Test
• Scoliosis Monitoring (scripted, bundled in Scoliosis extension)
• Slicer MRBSave Restore Check Paths Test
• CLIROITest (cli, built-in)
• Performance Tests
• Slicer MRBMultiple Save Restore Test
• Slicer MRBTest
• SEGExporter Self Test
• Self Tests
• Slicer MRBMultiple Save Restore Loop Test

IGT Tests

• Breach Warning Self Test
• Watchdog Self Test

SlicerRT Tests

• IGRTWorkflow Self Test
• Dicom Rt Import Self Test
• Batch Structure Set Conversion (scripted, bundled in Slicer RT extension)

TestCases

• Atlas Tests
• Add Storable Data After Scene View Test
• test tractography display
• RSNAQuant Tutorial
• Neurosurgical Planning Tutorial Markups Self Test
• Change Tracker Self Test
• Fiducial Layout Switch Bug1914
• Graph Cut Segment Self Test
• Charting (scripted, built-in)
• Cardiac Agatston Measures (scripted, bundled in Cardiac Agatston Measures extension)
• fiber visibility crash2438
• RSNAVis Tutorial
• JRC2013Vis
• Add Many Markups Fiducial Test
• Slicer4Minute (scripted, built-in)
• Crop Volume Self Test
• Slice Link Logic (scripted, built-in)
• Volume Rendering Scene Close (scripted, built-in)
• slicer Close Crash Bug2590
• CLIEvent Test
• Markups Widgets Self Test
• Tables Self Test
• Markups In Views Self Test
• Two CLIs In Parallel Test
• Subject Hierarchy Core Plugins Self Test
• Subject Hierarchy Generic Self Test
• Scene Performance (scripted, built-in)
• Markups In Compare Viewers Self Test
• scene Import2428
• RSNA2012Prostate Demo
• DTINot Reproducible Issue3977
• Two CLIs In ARow Test
• Colors Scalar Bar Self Test
• BRAINSFit Rigid Registration Crash Issue4139
• View Controllers Slice Interpolation Bug1926

Utilities

• Data Store (loadable, built-in)
• BRAINSStrip Rotation (cli, built-in)
• EMSegment Transform To New Format (cli, built-in)

BRAINS

• BRAINSTransform Convert (cli, built-in)

Vascular Modeling Toolkit

• Centerline Computation (scripted, bundled in VMTK extension)
• Vesselness Filtering (scripted, bundled in VMTK extension)
• Level Set Segmentation (scripted, bundled in VMTK extension)

Wizards

• Compare Volumes (scripted, built-in)
• Change Tracker (scripted, bundled in Change Tracker extension)

Modules by name

311 modules:

• ABC (cli, bundled in ABC extension)
• ACPCTransform (cli, built-in)
• Add Scalar Volumes (cli, built-in)
• Airway Inspector (loadable, bundled in Chest Imaging Platform extension)
• Airway Segmentation (scripted, bundled in Airway Segmentation extension)
• Airway Segmentation CLI (cli, bundled in Airway Segmentation extension)
• Angle Planes (scripted, bundled in Angle Planes Extension extension)
• Annotations (loadable, built-in)
• Apply Matrix (cli, bundled in CMFreg extension)
• Beams (loadable, bundled in Slicer RT extension)
• Bin Shrink (cli, bundled in IASEM extension)
• Body Centric Cubic Mesh (cli, bundled in CBC 3D I2MConversion extension)
• BRAINSDemon Warp (cli, built-in)
• BRAINSDWICleanup (cli, built-in)
• BRAINSFit (cli, built-in)
• BRAINSLabel Stats (cli, built-in)
• BRAINSResample (cli, built-in)
• BRAINSResize (cli, built-in)
• BRAINSROIAuto (cli, built-in)
• BRAINSStrip Rotation (cli, built-in)
• BRAINSTransform Convert (cli, built-in)
• Breach Warning (loadable, bundled in Slicer IGT extension)
• Breach Warning Light (scripted, bundled in Lump Nav extension)
• Carrera Slice (loadable, bundled in Carrera Slice extension)
• Cast Scalar Volume (cli, built-in)
• Centerline Computation (scripted, bundled in VMTK extension)
• Change Tracker (scripted, bundled in Change Tracker extension)
• Checker Board Filter (cli, built-in)
• CIP Body Composition (scripted, bundled in Chest Imaging Platform extension)
• CIP Common (scripted, bundled in Chest Imaging Platform extension)
• CIP Lesion Model (scripted, bundled in Chest Imaging Platform extension)
• CIP MIPViewer (scripted, bundled in Chest Imaging Platform extension)
• CIP PAARatio (scripted, bundled in Chest Imaging Platform extension)
• CIP Parenchyma Subtype Training (scripted, bundled in Chest Imaging Platform extension)
• CIP Trachea Stent Planning (scripted, bundled in Chest Imaging Platform extension)
• Classify Fissure Particles (cli, bundled in Chest Imaging Platform extension)
• Cleaver CLI (cli, bundled in Cleaver Extension extension)
• CMRToolkit Automatic Left Atrial Scar (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Axial Dilate (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Boolean REMOVEFilter (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Connected Threshold Filter (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Inhomogeneity Correction (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Isolated Connected Filter (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit LASegmentation Graph Cuts (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit PVAntrum Cut (cli, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Registration (scripted, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Registration BRAINSFit (scripted, bundled in Cardiac MRI Toolkit extension)
• CMRToolkit Wizard (scripted, bundled in Cardiac MRI Toolkit extension)
• Collect Fiducials (loadable, bundled in Slicer IGT extension)
• Colors (loadable, built-in)
• Compare Volumes (scripted, built-in)
• Compute Cross Sectional Area (cli, bundled in Chest Imaging Platform extension)
• Compute Distance Map (cli, bundled in Chest Imaging Platform extension)
• Compute Feature Strength (cli, bundled in Chest Imaging Platform extension)
• Compute Fissure Feature Vectors (cli, bundled in Chest Imaging Platform extension)
• Compute Intensity Statistics (cli, bundled in Chest Imaging Platform extension)
• Convert Chest Region Chest Type To Label Map Value (cli, bundled in Chest Imaging Platform extension)
• Convert Dicom (cli, bundled in Chest Imaging Platform extension)
• Convert Label Map Value To Chest Region Chest Type (cli, bundled in Chest Imaging Platform extension)
• Convert VTK (cli, bundled in UKFTractography extension)
• Corner Annotation (scripted, bundled in Corner Annotation extension)
• Create DICOMSeries (cli, built-in)
• Create Models (loadable, bundled in Slicer IGT extension)
• Crop Lung (cli, bundled in Chest Imaging Platform extension)
• Crop Volume (loadable, built-in)
• Curvature Anisotropic Diffusion (cli, built-in)
• Curve Maker (scripted, bundled in Curve Maker extension)
• Data (loadable, built-in)
• Data Probe (scripted, built-in)
• Data Store (loadable, built-in)
• Dice Computation (loadable, bundled in Dice Computation extension)
• DICOM (scripted, built-in)
• DICOM2Full Brain Tractography (scripted, built-in)
• Dicom Rt Import Export (loadable, bundled in Slicer RT extension)
• Dicom Sro Export (scripted, bundled in Slicer RT extension)
• Dicom Sro Import (loadable, bundled in Slicer RT extension)
• Diffusion Tensor Scalar Measurements (cli, built-in)
• Diffusion Weighted Volume Masking (cli, built-in)
• Distance Map Based Registration (scripted, bundled in Slicer Prostate extension)
• Dose Accumulation (loadable, bundled in Slicer RT extension)
• Dose Comparison (loadable, bundled in Slicer RT extension)
• Dose Morphology (loadable, bundled in Margin Calculator extension)
• Dose Population Histogram (loadable, bundled in Margin Calculator extension)
• Dose Volume Histogram (loadable, bundled in Slicer RT extension)
• Downsize (cli, bundled in CMFreg extension)
• d Pet Brain Quantification (scripted, bundled in Pet Spect Analysis extension)
• DSCMRIAnalysis (cli, bundled in DSCMRIAnalysis extension)
• Dvh Comparison (scripted, bundled in Slicer RT extension)
• DWIConvert (cli, built-in)
• DWITo DTIEstimation (cli, built-in)
• DWModeling (cli, bundled in Slicer Prostate extension)
• Easy Clip (scripted, bundled in Easy Clip extension)
• Editor (scripted, built-in)
• EMSegment (loadable, built-in)
• EMSegment Command Line (cli, built-in)
• EMSegment Quick (loadable, built-in)
• EMSegment Transform To New Format (cli, built-in)
• Encode SEG (cli, bundled in Reporting extension)
• Endoscopy (scripted, built-in)
• Enhance Fissures In Image (cli, bundled in Chest Imaging Platform extension)
• Evaluate Lung Lobe Segmentation Results (cli, bundled in Chest Imaging Platform extension)
• Execute System Command (cli, bundled in Chest Imaging Platform extension)
• Extract Chest Label Map (cli, bundled in Chest Imaging Platform extension)
• Extract Fissure Boundary From Lobe Map (cli, bundled in Chest Imaging Platform extension)
• Extract Particles From Chest Region Chest Type (cli, bundled in Chest Imaging Platform extension)
• Extract Skeleton (cli, built-in)
• Fast Grow Cut (loadable, bundled in Fast Grow Cut Effect extension)
• Fast Grow Cut Segmenter (loadable, bundled in Carrera Slice extension)
• Fiber Bundle Label Select (cli, built-in)
• Fiber Bundle To Label Map (scripted, built-in)
• Fiber Tract Measurements (cli, built-in)
• Fiducial Registration (cli, built-in)
• Fiducial Registration Wizard (loadable, bundled in Slicer IGT extension)
• Fiducials To Model Registration (scripted, bundled in Slicer IGT extension)
• Filter Airway Particle Data (cli, bundled in Chest Imaging Platform extension)
• Filter Connected Components (cli, bundled in Chest Imaging Platform extension)
• Filter Fissure Particle Data (cli, bundled in Chest Imaging Platform extension)
• Filter Vessel Particle Data (cli, bundled in Chest Imaging Platform extension)
• Find Patch Match (cli, bundled in Chest Imaging Platform extension)
• Finsler Backtracing (cli, bundled in Finsler Tractography extension)
• Finsler Tractography (cli, bundled in Finsler Tractography extension)
• Fit Lobe Surface Models To Particle Data (cli, bundled in Chest Imaging Platform extension)
• Gaussian Blur Image Filter (cli, built-in)
• Gel Dosimetry Analysis (scripted, bundled in Gel Dosimetry Analysis extension)
• Gel Dosimetry Analysis Algo (loadable, bundled in Gel Dosimetry Analysis extension)
• Generate Atlas Convex Hull (cli, bundled in Chest Imaging Platform extension)
• Generate Binary Thinning3D (cli, bundled in Chest Imaging Platform extension)
• Generate Distance Map From Label Map (cli, bundled in Chest Imaging Platform extension)
• Generate Image Sub Volumes (cli, bundled in Chest Imaging Platform extension)
• Generate Lesion Segmentation (cli, bundled in Chest Imaging Platform extension)
• Generate Lobe Surface Models (cli, bundled in Chest Imaging Platform extension)
• Generate Median Filtered Image (cli, bundled in Chest Imaging Platform extension)
• Generate NLMFiltered Image (cli, bundled in Chest Imaging Platform extension)
• Generate Otsu Lung Cast (cli, bundled in Chest Imaging Platform extension)
• Generate Overlay Images (cli, bundled in Chest Imaging Platform extension)
• Generate Partial Lung Label Map (cli, bundled in Chest Imaging Platform extension)
• Generate Region Histograms And Parenchyma Phenotypes (cli, bundled in Chest Imaging Platform extension)
• Generate Stenciled Label Map From Particles (cli, bundled in Chest Imaging Platform extension)
• Get Structures In Label Map (cli, bundled in Chest Imaging Platform extension)
• Get Transformation Kappa (cli, bundled in Chest Imaging Platform extension)
• Get Transformation Kappa2D (cli, bundled in Chest Imaging Platform extension)
• Get Transformation Similarity Metric (cli, bundled in Chest Imaging Platform extension)
• Gradient Anisotropic Diffusion (cli, built-in)
• Graph Cut Interactive Segmenter (loadable, bundled in Graph Cut Segment extension)
• Grayscale Fill Hole Image Filter (cli, built-in)
• Grayscale Grind Peak Image Filter (cli, built-in)
• Grayscale Model Maker (cli, built-in)
• Growing (cli, bundled in CMFreg extension)
• Gyro Guide (scripted, bundled in Gyro Guide extension)
• Heterogeneity CAD (scripted, bundled in Open CAD extension)
• Histogram Matching (cli, built-in)
• IASEMImport (cli, bundled in IASEM extension)
• IASEMImport Series (cli, bundled in IASEM extension)
• i Gyne (scripted, bundled in i Gyne extension)
• Image Label Combine (cli, built-in)
• Intensity Difference Metric (cli, bundled in Change Tracker extension)
• Intensity Segmenter (cli, bundled in Intensity Segmenter extension)
• Interactive Lobe Segmentation (scripted, bundled in Chest Imaging Platform extension)
• Island Removal (cli, built-in)
• Isodose (loadable, bundled in Slicer RT extension)
• KUtil (scripted, bundled in Carrera Slice extension)
• Label Addition (cli, bundled in CMFreg extension)
• Label Extraction (cli, bundled in CMFreg extension)
• Label Map From Region And Type Points (cli, bundled in Chest Imaging Platform extension)
• Label Map Smoothing (cli, built-in)
• Label Object Statistics (scripted, bundled in IASEM extension)
• Label Particles By Chest Region Chest Type (cli, bundled in Chest Imaging Platform extension)
• Label Statistics (scripted, built-in)
• Landmark Registration (scripted, built-in)
• LAScar Segmenter (cli, bundled in LAScar Segmenter extension)
• LASegmentation Workflow (scripted, bundled in Cardiac MRI Toolkit extension)
• Level Set Segmentation (scripted, bundled in VMTK extension)
• Lump Nav (scripted, bundled in Lump Nav extension)
• Margin Calculator (scripted, bundled in Margin Calculator extension)
• Markups (loadable, built-in)
• Markups To Model (loadable, bundled in Slicer IGT extension)
• Mask Creation (cli, bundled in CMFreg extension)
• Mask Out Label Map Structures (cli, bundled in Chest Imaging Platform extension)
• Mask Scalar Volume (cli, built-in)
• Median Image Filter (cli, built-in)
• Merge Chest Label Maps (cli, bundled in Chest Imaging Platform extension)
• Merge Models (cli, built-in)
• Merge Particle Data Sets (cli, bundled in Chest Imaging Platform extension)
• Mesh Compression (cli, bundled in CBC 3D I2MConversion extension)
• Mesh To Label Map (cli, bundled in Mesh To Label Map extension)
• Metafile Importer (loadable, bundled in Sequences extension)
• Model Maker (cli, built-in)
• Model Registration (scripted, bundled in Slicer IGT extension)
• Models (loadable, built-in)
• Model To Label Map (cli, built-in)
• Model To Model Distance (cli, bundled in Model To Model Distance extension)
• Motion Simulator (loadable, bundled in Margin Calculator extension)
• Motion Simulator Double Array (loadable, bundled in Margin Calculator extension)
• mp Review (scripted, bundled in mp Review extension)
• mp Review Preprocessor (scripted, bundled in mp Review extension)
• Multiply Scalar Volumes (cli, built-in)
• Multi Volume Explorer (loadable, built-in)
• Multi Volume Importer (scripted, built-in)
• N4ITKBias Field Correction (cli, built-in)
• Needle Finder (scripted, bundled in Needle Finder extension)
• Non Growing (cli, bundled in CMFreg extension)
• Open IGTLink IF (loadable, built-in)
• Open IGTLink Remote (loadable, bundled in Slicer IGT extension)
• Orient Scalar Volume (cli, built-in)
• Particles Display (loadable, bundled in Chest Imaging Platform extension)
• Path Explorer (loadable, bundled in Slicer IGT extension)
• PBNRR (cli, bundled in PBNRR extension)
• Perform Metric Test (cli, built-in)
• Perform Morphological (cli, bundled in Chest Imaging Platform extension)
• Perturb Particles (cli, bundled in Chest Imaging Platform extension)
• PETIndi C (scripted, bundled in PET-Indi C extension)
• PETStandard Uptake Value Computation (cli, built-in)
• PETSUVImage Maker (cli, bundled in Longitudinal PETCT extension)
• PETTumor Segmentation (loadable, bundled in PETTumor Segmentation extension)
• Philips4d Us Dicom Patcher (scripted, bundled in Slicer Heart extension)
• Pick And Paint (scripted, bundled in Pick And Paint Extension extension)
• Pivot Calibration (loadable, bundled in Slicer IGT extension)
• Pk Modeling (cli, bundled in Pk Modeling extension)
• Planar Image (loadable, bundled in Slicer RT extension)
• plastimatch slicer bspline (cli, bundled in Slicer RT extension)
• plastimatch slicer landwarp (cli, bundled in Slicer RT extension)
• Plastimatch Py (loadable, bundled in Slicer RT extension)
• Plm Register (scripted, bundled in Slicer RT extension)
• Plus Remote (scripted, bundled in Slicer IGT extension)
• Probe Volume With Model (cli, built-in)
• Q3DC (scripted, bundled in Q3DC extension)
• Quad Edge Surface Mesher (cli, bundled in Slicer Prostate extension)
• Quality Control (cli, bundled in Chest Imaging Platform extension)
• Quantitative Indices CLI (cli, bundled in PET-Indi C extension)
• Quantitative Indices Tool (scripted, bundled in PET-Indi C extension)
• Read Dicom Write Tags (cli, bundled in Chest Imaging Platform extension)
• Read NRRDs Write VTK (cli, bundled in Chest Imaging Platform extension)
• Read Vida Write CIP (cli, bundled in Chest Imaging Platform extension)
• Read VTKWrite NRRDs (cli, bundled in Chest Imaging Platform extension)
• Read Write Image Data (cli, bundled in Chest Imaging Platform extension)
• Read Write Region And Type Points (cli, bundled in Chest Imaging Platform extension)
• Reformat (loadable, built-in)
• Region Type (loadable, bundled in Chest Imaging Platform extension)
• Region Type Locations To ROIVolume (cli, bundled in Chest Imaging Platform extension)
• Register CT (cli, bundled in Chest Imaging Platform extension)
• Register Label Maps (cli, bundled in Chest Imaging Platform extension)
• Register Lung Atlas (cli, bundled in Chest Imaging Platform extension)
• Remap Label Map (cli, bundled in Chest Imaging Platform extension)
• Remove Chest Type From Label Map Using Particles (cli, bundled in Chest Imaging Platform extension)
• Remove Particles From Particles Data Set (cli, bundled in Chest Imaging Platform extension)
• Resample CT (cli, bundled in Chest Imaging Platform extension)
• Resample DTIlog Euclidean (cli, bundled in Resample DTIlog Euclidean extension)
• Resample DTIVolume (cli, built-in)
• Resample Label Map (cli, bundled in Chest Imaging Platform extension)
• Resample Scalar Vector DWIVolume (cli, built-in)
• Rescale Label Map (cli, bundled in Chest Imaging Platform extension)
• Robust Statistics Segmenter (cli, built-in)
• Sample Data (scripted, built-in)
• Scar Visualization (scripted, bundled in Cardiac MRI Toolkit extension)
• Scene Views (loadable, built-in)
• SEG2NRRD (cli, bundled in Reporting extension)
• Segmentations (loadable, bundled in Slicer RT extension)
• Segmentation Smoothing (cli, bundled in Slicer Prostate extension)
• Segment CAD (scripted, bundled in Open CAD extension)
• Segment Comparison (loadable, bundled in Slicer RT extension)
• Segment Editor (scripted, bundled in Slicer RT extension)
• Segment Lung Lobes (cli, bundled in Chest Imaging Platform extension)
• Segment Morphology (loadable, bundled in Slicer RT extension)
• Sequence Browser (loadable, bundled in Sequences extension)
• Sequences (loadable, bundled in Sequences extension)
• Simple Filters (scripted, built-in)
• Simple Region Growing Segmentation (cli, built-in)
• Skull Stripper (cli, bundled in Skull Stripper extension)
• Slicer To Kiwi Exporter (scripted, bundled in Slicer To Kiwi Exporter extension)
• Spacing Aware Curvature Diffusion (cli, bundled in IASEM extension)
• Spinal Curvature Measurement (scripted, bundled in Scoliosis extension)
• Split Left Lung Right Lung (cli, bundled in Chest Imaging Platform extension)
• Subject Hierarchy (loadable, built-in)
• Subtract Scalar Volumes (cli, built-in)
• Surface Registration (scripted, bundled in CMFreg extension)
• Surface Toolbox (scripted, built-in)
• SUVFactor Calculator (cli, bundled in PETDICOMExtension extension)
• Swiss Skull Stripper (cli, bundled in Swiss Skull Stripper extension)
• Synthetic RTDose (scripted, bundled in Margin Calculator extension)
• T1Mapping (cli, bundled in T1Mapping extension)
• Tables (loadable, built-in)
• TCIABrowser (scripted, bundled in TCIABrowser extension)
• Threshold Scalar Volume (cli, built-in)
• Tracker Stabilizer (loadable, bundled in Tracker Stabilizer extension)
• Tractography Display (loadable, built-in)
• Tractography Interactive Seeding (loadable, built-in)
• Tractography Label Map Seeding (cli, built-in)
• Transfer Region And Type Indices To From Points (cli, bundled in Chest Imaging Platform extension)
• Transform Fusion (loadable, bundled in Slicer IGT extension)
• Transforms (loadable, built-in)
• UKFTractography (cli, bundled in UKFTractography extension)
• Ultrasound Snapshots (loadable, bundled in Slicer IGT extension)
• Units (loadable, built-in)
• Valve View (scripted, bundled in Slicer Heart extension)
• VBRAINSDemon Warp (cli, built-in)
• Vector To Scalar Volume (scripted, built-in)
• Vesselness Filtering (scripted, bundled in VMTK extension)
• Vff File Reader (loadable, bundled in Slicer RT extension)
• View Controllers (loadable, built-in)
• Viewpoint (scripted, bundled in Lump Nav extension)
• Volume Clip With Model (scripted, bundled in Volume Clip extension)
• Volume Clip With Roi (scripted, bundled in Volume Clip extension)
• Volume Rendering (loadable, built-in)
• Volume Reslice Driver (loadable, bundled in Slicer IGT extension)
• Volumes (loadable, built-in)
• Voting Binary Hole Filling Image Filter (cli, built-in)
• Wasp (scripted, bundled in Wasp extension)
• Watchdog (loadable, bundled in Slicer IGT extension)
• Welcome (loadable, built-in)
• Window Level Effect (scripted, bundled in Window Level Effect extension)