Documentation/4.4

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

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Where to start ? Training pages Information on how to use Slicer 4.4 FAQ Set of common questions/answers Users mailing list / Sign-up / Browse archives How to Report a problem / Create a feature request  NEW Slicer Application Main Application GUI Settings  NEW Extensions Manager  NEW Mouse Buttons, "Hot-keys" and Keyboard Shortcuts 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 Developers mailing list / Browse archives Intended for discussion of programming related questions 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 Slicer Registration Case Library Real-life example cases of using the Slicer registration tools, incl. datasets and step-by-step instructions to follow and try yourself. Documentación en Español   NEW Introducción a 3D Slicer en Español Breve descripción de proyecto y un breve viaje por sus principales herramientas y funcionalidades. Reconstrucciones volumétricas con 3D Slicer Guía de uso para la herramienta de creación de reconstrucciones volumétricas de 3D Slicer. Crear modelos/contornos de órganos con 3D Slicer Guía rápida introductoria para la creación de contornos de órganos para generar vistas volumétricas. Endoscopías virtuales con 3D Slicer Manual de uso de la herramienta para 3D Slicer desarrollada por Steve Pieper para realizar endoscopías virtuales. Creando curvas de isodosis con SlicerRT de 3D Slicer Introducción a la extensión SlicerRT para 3D Slicer enfocada en investigación en radioterapia.

Modules by category

36 categories:

• BRAINS
  • Label Statistics
• Cardiac MRI Toolkit
• 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
• File
• 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
• Multidimensional data
• Multi Volume Support
• Perk Tutor
• Plastimatch
  • Registration
  • Utilities
• Quantification
  • Change Quantification
• Radiotherapy
• Registration
  • Specialized
• Segmentation
  • Specialized
• Shape Analysis
  • CMF Registration
    • Voxelbase Registration
• Slicelets
• Surface Models
• Testing
  • IGT Tests
  • Slicer RT Tests
  • Test Cases
• Unspecified
• Utilities
  • BRAINS
• Vascular Modeling Toolkit
• Wizards
• Work in Progress
  • Converters
  • Informatics
    • Test Cases

BRAINS

LabelStatistics

• BRAINSLabel Stats (cli, built-in)

Cardiac MRI Toolkit

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

Converters

• Vector To Scalar Volume (scripted, built-in)
• Crop Volume (loadable, built-in)
• Create DICOMSeries (cli, built-in)
• Orient Scalar Volume (cli, built-in)

Developer Tools

• Event Broker
• Execution Model Tour (cli, built-in)
• Double Arrays (loadable, built-in)
• Cameras (loadable, built-in)
• Extension Stats (scripted, bundled in Developer Tools For Extensions extension)
• Developer Tools For Extensions (scripted, bundled in Developer Tools For Extensions extension)
• Extension Wizard (scripted, built-in)
• Image Maker (cli, bundled in Image Maker extension)

DICOM Plugins

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

Editor Extensions

• Binary Watershed Effect (scripted, bundled in IASEM extension)
• Double Threshold Effect (scripted, bundled in IASEM extension)
• PETTumor Segmentation Effect (scripted, bundled in PETTumor Segmentation extension)

Matlab

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

Diffusion

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

Diffusion Data Conversion

• DWIConvert (cli, built-in)

Diffusion Tensor Images

• Resample DTIVolume (cli, built-in)
• Diffusion Tensor Scalar Measurements (cli, built-in)
• Resample DTIlog Euclidean (cli, bundled in Resample DTIlog Euclidean extension)
• Tractography Label Map Seeding (cli, built-in)
• Tractography Interactive Seeding (loadable, built-in)

Diffusion Weighted Images

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

FiberAnalysis

• DTIAtlas Fiber Analyzer (cli, bundled in DTIAtlas Fiber Analyzer extension)
• Fiber Compare (cli, bundled in DTIAtlas Fiber Analyzer extension)
• Merge Stat With Fiber (cli, bundled in DTIAtlas Fiber Analyzer extension)
• dtitractstat (cli, bundled in DTIAtlas Fiber Analyzer extension)

Tractography

• Fiber Bundle To Label Map (scripted, built-in)
• Fiber Bundle Label Select (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)
• Segmentation Aided Registration (cli, bundled in Segmentation Aided Registration extension)
• Carrera Slice (loadable, bundled in Carrera Slice extension)

Exporter

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

File

• Convert VTK (cli, bundled in UKFTractography extension)

Filtering

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

Arithmetic

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

Denoising

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

Morphology

• Grayscale Fill Hole Image Filter (cli, built-in)
• Erode Label (cli, bundled in Erode Dilate Label extension)
• Grayscale Grind Peak Image Filter (cli, built-in)
• Dilate Label (cli, bundled in Erode Dilate Label extension)

IGT

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

Informatics

• Annotations (loadable, built-in)
• Markups (loadable, built-in)
• Units (loadable, built-in)
• DICOM (scripted, built-in)
• Sample Data (scripted, built-in)
• Subject Hierarchy (loadable, built-in)
• Data (loadable, built-in)
• Colors (loadable, built-in)
• Curve Maker (scripted, bundled in Curve Maker extension)
• TCIABrowser (scripted, bundled in TCIABrowser extension)

Legacy

Converters

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

Diffusion

Denoising

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

Diffusion Data Conversion

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

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

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

Multidimensional data

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

MultiVolume Support

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

Perk Tutor

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

• d Pet Brain Quantification (scripted, bundled in Pet Spect Analysis 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)
• PETIndi C (scripted, bundled in PET-Indi C extension)
• Pk Modeling (cli, bundled in Pk Modeling extension)
• Quantitative Indices Tool (scripted, bundled in PET-Indi C extension)
• Heterogeneity CAD (scripted, bundled in Open CAD extension)
• PETSUVImage Maker (cli, bundled in Longitudinal PETCT extension)
• Dice Computation (loadable, bundled in Dice Computation extension)
• Data Probe (scripted, built-in)

ChangeQuantification

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

Radiotherapy

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

Registration

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

Specialized

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

Segmentation

• Airway Segmentation (scripted, bundled in Airway Segmentation extension)
• IGR3D MABMIS Training (cli, bundled in MABMIS extension)
• Wasp (scripted, bundled in Wasp extension)
• ABC (cli, bundled in ABC extension)
• EMSegment Quick (loadable, built-in)
• Simple Region Growing Segmentation (cli, built-in)
• EMSegment (loadable, built-in)
• 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)
• Airway Segmentation CLI (cli, bundled in Airway Segmentation extension)
• LAScar Segmenter (cli, bundled in LAScar Segmenter extension)
• Sobolev Segmenter (cli, bundled in Sobolev Segmenter extension)
• Volume Clip With Model (scripted, bundled in Volume Clip extension)
• IGR3D MABMIS Testing (cli, bundled in MABMIS extension)
• Intensity Segmenter (cli, bundled in Intensity Segmenter extension)

Specialized

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

Shape Analysis

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

CMF Registration

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

Voxelbase Registration

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

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

Testing

• Self Tests
• CLIROITest (cli, built-in)
• CLI4Test
• Threshold Threading Test
• Scoliosis Monitoring (scripted, bundled in Scoliosis extension)
• Performance Tests
• Slicer MRBTest

IGT Tests

• Breach Warning Self Test
• Watchdog Self Test

SlicerRT Tests

• NAMIC Tutorial 2013June Self Test
• Dicom Rt Import Self Test
• Batch Contour Conversion (scripted, bundled in Slicer RT extension)

TestCases

• Slice Link Logic (scripted, built-in)
• Atlas Tests
• RSNAQuant Tutorial
• Volume Rendering Scene Close (scripted, built-in)
• test tractography display
• slicer Close Crash Bug2590
• Subject Hierarchy Generic Self Test
• Scene Performance (scripted, built-in)
• Charting (scripted, built-in)
• Neurosurgical Planning Tutorial Markups Self Test
• Markups In Compare Viewers Self Test
• Cardiac Agatston Measures (scripted, bundled in Cardiac Agatston Measures extension)
• fiber visibility crash2438
• scene Import2428
• RSNAVis Tutorial
• JRC2013Vis
• RSNA2012Prostate Demo
• Add Many Markups Fiducial Test
• Colors Scalar Bar Self Test
• Markups In Views Self Test
• Subject Hierarchy Core Plugins Self Test
• Change Tracker Self Test
• Fiducial Layout Switch Bug1914
• View Controllers Slice Interpolation Bug1926
• Slicer4Minute (scripted, built-in)
• label Toggle Bug2049

Unspecified

• BRAINSDWICleanup (cli, built-in)

Utilities

• Thingiverse Browser (scripted, bundled in Thingiverse Browser extension)
• BRAINSStrip Rotation (cli, built-in)
• EMSegment Transform To New Format (cli, built-in)
• Data Store (loadable, built-in)

BRAINS

• BRAINSTransform Convert (cli, built-in)

Vascular Modeling Toolkit

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

TestCases

• Reporting Self Test
• Label To DICOMSEGConverter Self Test

Modules by name

233 modules:

• ABC (cli, bundled in ABC extension)
• ACPCTransform (cli, built-in)
• Add Scalar Volumes (cli, built-in)
• 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)
• 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)
• 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 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)
• Contour Comparison (loadable, bundled in Slicer RT extension)
• Contour Morphology (loadable, bundled in Slicer RT extension)
• Contours (loadable, bundled in Slicer RT 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 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 Export (loadable, bundled in Slicer RT extension)
• Dicom Rt Import (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)
• Dilate Label (cli, bundled in Erode Dilate Label 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)
• DTIAtlas Fiber Analyzer (cli, bundled in DTIAtlas Fiber Analyzer extension)
• dtitractstat (cli, bundled in DTIAtlas Fiber Analyzer 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)
• Easy Clip (scripted, bundled in Easy Clip extension)
• 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)
• Erode Label (cli, bundled in Erode Dilate Label 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 Compare (cli, bundled in DTIAtlas Fiber Analyzer extension)
• Fiducial Registration (cli, built-in)
• Fiducial Registration Wizard (loadable, bundled in Slicer IGT extension)
• Fiducials To Model Registration (scripted, bundled in Slicer IGT extension)
• Finsler Backtracing (cli, bundled in Finsler Tractography extension)
• Finsler Tractography (cli, bundled in Finsler Tractography 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)
• Gradient Anisotropic Diffusion (cli, built-in)
• 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)
• IGR3D MABMIS Testing (cli, bundled in MABMIS extension)
• IGR3D MABMIS Training (cli, bundled in MABMIS 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)
• 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 Smoothing (cli, built-in)
• Label Object Statistics (scripted, bundled in IASEM extension)
• 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)
• Longitudinal PETCT (loadable, bundled in Longitudinal PETCT extension)
• Margin Calculator (scripted, bundled in Margin Calculator extension)
• Markups (loadable, built-in)
• Mask Creation (cli, bundled in CMFreg extension)
• Mask Scalar Volume (cli, built-in)
• Median Image Filter (cli, built-in)
• Merge Models (cli, built-in)
• Merge Stat With Fiber (cli, bundled in DTIAtlas Fiber Analyzer 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 Multidim Data 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)
• Path Explorer (loadable, bundled in Slicer IGT extension)
• PBNRR (cli, bundled in PBNRR extension)
• Percutaneous Approach Analysis (scripted, bundled in Percutaneous Approach Analysis extension)
• Perform Metric Test (cli, built-in)
• Perk Evaluator (loadable, bundled in Perk Tutor 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)
• 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)
• Port Placement (scripted, bundled in Port Placement extension)
• Probe Volume With Model (cli, built-in)
• Python Metrics Calculator (scripted, bundled in Perk Tutor extension)
• Q3DC (scripted, bundled in Q3DC extension)
• Quantitative Indices CLI (cli, bundled in PET-Indi C extension)
• Quantitative Indices Tool (scripted, bundled in PET-Indi C extension)
• Reformat (loadable, built-in)
• Reporting (loadable, bundled in Reporting extension)
• Resample DTIlog Euclidean (cli, bundled in Resample DTIlog Euclidean extension)
• Resample DTIVolume (cli, built-in)
• Resample Scalar Vector DWIVolume (cli, built-in)
• Resection Volume (scripted, bundled in Resection Planner 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)
• Segmentation Aided Registration (cli, bundled in Segmentation Aided Registration extension)
• Segment CAD (scripted, bundled in Open CAD extension)
• Sequence Browser (loadable, bundled in Multidim Data extension)
• Sequences (loadable, bundled in Multidim Data extension)
• Simple Filters (scripted, built-in)
• Simple Region Growing Segmentation (cli, built-in)
• Slicer To Kiwi Exporter (scripted, bundled in Slicer To Kiwi Exporter extension)
• Sobolev Segmenter (cli, bundled in Sobolev Segmenter extension)
• Spacing Aware Curvature Diffusion (cli, bundled in IASEM extension)
• Spinal Curvature Measurement (scripted, bundled in Scoliosis 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)
• TCIABrowser (scripted, bundled in TCIABrowser extension)
• Thingiverse Browser (scripted, bundled in Thingiverse Browser 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)
• 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)
• 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)
• 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)