Documentation/4.5/Modules

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

Modules by category

37 categories:

• Cardiac
• Cardiac MRI Toolkit
• Chest Imaging Platform
  • Toolkit
    • General
    • 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
  • Fiber Analysis
  • Tractography
• Editor Effects
• Editor Effect
• Endoscopy
• Examples
• Exporter
• Filter
• Filtering
  • Arithmetic
  • Denoising
  • Morphology
• IGT
• Informatics
• Legacy
  • Converters
  • Diffusion
    • Denoising
    • Diffusion Data Conversion
  • Filtering
  • Registration
  • Work in Progress
    • Diffusion Tensor
      • Test
• Margin Calculator
• Mesh Generation
• Mesh Generation
• Microscopy
• Multi Volume Support
• Perk Tutor
• Plastimatch
  • Registration
  • Utilities
• Quantification
  • Change Quantification
• Radiotherapy
• Registration
  • Label Registration
  • Specialized
• Segmentation
  • Specialized
• Sequences
• Shape Analysis
  • CMF Registration
    • Voxelbase Registration
• Slicelets
• Surface Models
• Testing
  • IGT Tests
  • Slicer RT Tests
  • Test Cases
• Utilities
  • BRAINS
• Vascular Modeling Toolkit
• Wizards
• Work in Progress
  • Converters
  • Informatics
    • Test Cases

Cardiac

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

Toolkit

General

• Execute System Command (cli, bundled in Chest Imaging Platform extension)

Particles

• Scour Particle Data (cli, bundled in Chest Imaging Platform extension)
• 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)
• Transfer Field Data To From Point 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 Lesion Segmentation (cli, bundled in Chest Imaging Platform extension)
• Generate Binary Thinning3D (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)
• 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

• Tractography Display (loadable, built-in)
• DICOM2Full Brain Tractography (scripted, built-in)

Diffusion Data Conversion

• DWIConvert (cli, built-in)

Diffusion Tensor Images

• Resample DTIlog Euclidean (cli, bundled in Resample DTIlog Euclidean extension)
• Diffusion Tensor Scalar Measurements (cli, built-in)
• Resample DTIVolume (cli, built-in)

Diffusion Weighted Images

• DWIRician LMMSEFilter (cli, built-in)
• DWIJoint Rician LMMSEFilter (cli, built-in)
• Finsler Backtracing (cli, bundled in Finsler Tractography extension)
• Finsler Tractography (cli, bundled in Finsler Tractography extension)
• BRAINSDWICleanup (cli, built-in)
• DWITo DTIEstimation (cli, built-in)
• Diffusion Weighted Volume Masking (cli, built-in)
• Resample Scalar Vector DWIVolume (cli, built-in)

Tractography

• Tractography Interactive Seeding (loadable, built-in)
• Tractography Label Map Seeding (cli, built-in)
• Fiber Bundle Label Selection (cli, built-in)
• Fiber Bundle To Label Map (cli, built-in)
• Fiber Tract Measurements (cli, built-in)
• UKFTractography (cli, bundled in UKFTractography extension)

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)
• Graph Cut Interactive Segmenter (loadable, bundled in Graph Cut Segment extension)
• Carrera Slice (loadable, bundled in Carrera Slice 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)
• Light Weight Robot IGT (loadable, bundled in Light Weight Robot IGT 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

• TCIABrowser (scripted, bundled in TCIABrowser 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)
• mpReview (scripted, built-in)

Legacy

Converters

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

Diffusion

Denoising

• DWIUnbiased Non Local Means Filter (cli, built-in)

Diffusion Data Conversion

• DTIexport (cli, built-in)
• DTIimport (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

• Motion Simulator Double Array (loadable, bundled in Margin Calculator extension)
• 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)

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)

Perk Tutor

• Python Metrics Calculator (scripted, bundled in Perk Tutor extension)
• Transform Recorder (loadable, bundled in Perk Tutor extension)
• Perk Evaluator (loadable, bundled in Perk Tutor extension)
• Workflow Segmentation (loadable, bundled in Perk Tutor extension)

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

• PETIndi C (scripted, bundled in PET-Indi C 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)
• d Pet Brain Quantification (scripted, bundled in Pet Spect Analysis 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)

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)
• 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

• Q3DC (scripted, bundled in Q3DC extension)
• Mesh Statistics (scripted, bundled in Mesh Statistics Extension extension)
• Easy Clip (scripted, bundled in Easy Clip extension)
• Mesh To Label Map (cli, bundled in Mesh To Label Map extension)
• Model To Model Distance (cli, bundled in Model To Model Distance extension)
• Angle Planes (scripted, bundled in Angle Planes Extension extension)
• Pick And Paint (scripted, bundled in Pick And Paint Extension extension)

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)

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)
• Label Map Smoothing (cli, built-in)
• Probe Volume With Model (cli, built-in)

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 MRBTest
• Slicer MRBMultiple Save Restore 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
• 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
• Markups In Views Self 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
• Colors Scalar Bar Self Test
• 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)

Work in Progress

• Longitudinal PETCT (loadable, bundled in Longitudinal PETCT extension)

Converters

• Label To DICOMSEGConverter (scripted, bundled in Reporting extension)

Informatics

• Reporting (loadable, bundled in Reporting extension)

• mpReview (scripted, bundled in mpReview extension)

TestCases

• Label To DICOMSEGConverter Self Test
• Reporting Self Test

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 Common (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)
• Dvh Comparison (scripted, bundled in Slicer RT extension)
• DWIConvert (cli, built-in)
• DWIJoint Rician LMMSEFilter (cli, built-in)
• DWIRician LMMSEFilter (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)
• 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)
• Label To DICOMSEGConverter (scripted, bundled in Reporting extension)
• 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)
• Light Weight Robot IGT (loadable, bundled in Light Weight Robot IGT extension)
• Longitudinal PETCT (loadable, bundled in Longitudinal PETCT 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 Statistics (scripted, bundled in Mesh Statistics Extension 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)
• 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)
• Perk Evaluator (loadable, bundled in Perk Tutor 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)
• Python Metrics Calculator (scripted, bundled in Perk Tutor extension)
• 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)
• Reporting (loadable, bundled in Reporting 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)
• Scour Particle Data (cli, bundled in Chest Imaging Platform 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 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
• 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 Field Data To From Point Data (cli, bundled in Chest Imaging Platform extension)
• Transfer Region And Type Indices To From Points (cli, bundled in Chest Imaging Platform extension)
• Transform Fusion (loadable, bundled in Slicer IGT extension)
• Transform Recorder (loadable, bundled in Perk Tutor 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)
• Workflow Segmentation (loadable, bundled in Perk Tutor extension)