Modules by name

156 modules:

ABC (bundled in ABC extension)
ACPCTransform (built-in)
Add Scalar Volumes (built-in)
Airway Segmentation CLI (bundled in Airway Segmentation extension)
Annotations (built-in)
Apply Matrix (bundled in CMFreg extension)
Bin Shrink (bundled in IASEM extension)
Body Centric Cubic Mesh (bundled in CBC 3D I2MConversion extension)
BRAINSDemon Warp (built-in)
BRAINSDWICleanup (built-in)
BRAINSFit (built-in)
BRAINSLabel Stats (built-in)
BRAINSResample (built-in)
BRAINSResize (built-in)
BRAINSROIAuto (built-in)
BRAINSTransform Convert (built-in)
Carrera Slice (bundled in Carrera Slice extension)
Cast Scalar Volume (built-in)
Change Tracker (bundled in Change Tracker extension)
Checker Board Filter (built-in)
Cleaver CLI (bundled in Cleaver Extension extension)
Colors (built-in)
Compare Volumes (bundled in CMFreg extension)
Corner Annotation (bundled in Corner Annotation extension)
Create DICOMSeries (built-in)
Crop Volume (built-in)
Curvature Anisotropic Diffusion (built-in)
Curve Maker (bundled in Curve Maker extension)
Data (built-in)
Data Probe (built-in)
Data Store (built-in)
Dice Computation (bundled in Dice Computation extension)
DICOM (built-in)
DICOM2Full Brain Tractography (built-in)
Diffusion Tensor Scalar Measurements (built-in)
Diffusion Weighted Volume Masking (built-in)
Dilate Label (bundled in Erode Dilate Label extension)
Downsize (bundled in CMFreg extension)
DWIConvert (built-in)
DWIJoint Rician LMMSEFilter (built-in)
DWIRician LMMSEFilter (built-in)
DWITo DTIEstimation (built-in)
Editor (built-in)
EMSegment (built-in)
EMSegment Command Line (built-in)
EMSegment Quick (built-in)
EMSegment Transform To New Format (built-in)
Endoscopy (built-in)
Erode Label (bundled in Erode Dilate Label extension)
Extract Skeleton (built-in)
Fast Grow Cut (bundled in Fast Grow Cut Effect extension)
Fast Grow Cut Segmenter (bundled in Carrera Slice extension)
Fiber Bundle Label Select (built-in)
Fiber Bundle To Label Map (built-in)
Fiducial Registration (built-in)
Finsler Backtracing (bundled in Finsler Tractography extension)
Finsler Tractography (bundled in Finsler Tractography extension)
Gaussian Blur Image Filter (built-in)
Gel Dosimetry Analysis Algo (bundled in Gel Dosimetry Analysis extension)
Gradient Anisotropic Diffusion (built-in)
Grayscale Fill Hole Image Filter (built-in)
Grayscale Grind Peak Image Filter (built-in)
Grayscale Model Maker (built-in)
Growing (bundled in CMFreg extension)
Gyro Guide (bundled in Gyro Guide extension)
Histogram Matching (built-in)
IASEMImport (bundled in IASEM extension)
IASEMImport Series (bundled in IASEM extension)
IGR3D MABMIS Testing (bundled in MABMIS extension)
IGR3D MABMIS Training (bundled in MABMIS extension)
i Gyne (bundled in i Gyne extension)
Image Label Combine (built-in)
Intensity Difference Metric (bundled in Change Tracker extension)
Intensity Segmenter (bundled in Intensity Segmenter extension)
KUtil (bundled in Carrera Slice extension)
Label Addition (bundled in CMFreg extension)
Label Extraction (bundled in CMFreg extension)
Label Map Smoothing (built-in)
Label Object Statistics (bundled in IASEM extension)
Label Statistics (built-in)
Label To DICOMSEGConverter (bundled in Reporting extension)
Landmark Registration (bundled in CMFreg extension)
LAScar Segmenter (bundled in LAScar Segmenter extension)
Longitudinal PETCT (bundled in Longitudinal PETCT extension)
Markups (built-in)
Mask Creation (bundled in CMFreg extension)
Mask Scalar Volume (built-in)
Median Image Filter (built-in)
Merge Models (built-in)
Mesh Compression (bundled in CBC 3D I2MConversion extension)
Metafile Importer (bundled in Multidim Data extension)
Model Maker (built-in)
Models (built-in)
Model To Label Map (built-in)
Multiply Scalar Volumes (built-in)
Multi Volume Explorer (built-in)
Multi Volume Importer (built-in)
N4ITKBias Field Correction (built-in)
Needle Finder (bundled in Needle Finder extension)
Non Growing (bundled in CMFreg extension)
Open IGTLink IF (built-in)
Orient Scalar Volume (built-in)
PBNRR (bundled in PBNRR extension)
Percutaneous Approach Analysis (bundled in Percutaneous Approach Analysis extension)
Perform Metric Test (built-in)
Perk Evaluator (bundled in Perk Tutor extension)
PETStandard Uptake Value Computation (built-in)
PETSUVImage Maker (bundled in Longitudinal PETCT extension)
Pk Modeling (bundled in Pk Modeling extension)
Port Placement (bundled in Port Placement extension)
Probe Volume With Model (built-in)
Python Metrics Calculator (bundled in Perk Tutor extension)
Reformat (built-in)
Reporting (bundled in Reporting extension)
Resample DTIVolume (built-in)
Resample Scalar Vector DWIVolume (built-in)
Robust Statistics Segmenter (built-in)
Sample Data (built-in)
Scene Views (built-in)
Segmentation Aided Registration (bundled in Segmentation Aided Registration extension)
Sequence Browser (bundled in Multidim Data extension)
Sequences (bundled in Multidim Data extension)
Simple Filters (built-in)
Simple Region Growing Segmentation (built-in)
Slicer To Kiwi Exporter (bundled in Slicer To Kiwi Exporter extension)
Sobolev Segmenter (bundled in Sobolev Segmenter extension)
Spacing Aware Curvature Diffusion (bundled in IASEM extension)
Spinal Curvature Measurement (bundled in Scoliosis extension)
Subject Hierarchy (built-in)
Subtract Scalar Volumes (built-in)
Surface Registration (bundled in CMFreg extension)
Surface Toolbox (built-in)
SUVFactor Calculator (bundled in PETDICOMExtension extension)
Swiss Skull Stripper (bundled in Swiss Skull Stripper extension)
TCIABrowser (bundled in TCIABrowser extension)
Thingiverse Browser (bundled in Thingiverse Browser extension)
Threshold Scalar Volume (built-in)
Tracker Stabilizer (bundled in Tracker Stabilizer extension)
Tractography Display (built-in)
Tractography Interactive Seeding (built-in)
Tractography Label Map Seeding (built-in)
Transform Recorder (bundled in Perk Tutor extension)
Transforms (built-in)
Units (built-in)
VBRAINSDemon Warp (built-in)
Vector To Scalar Volume (built-in)
View Controllers (built-in)
Volume Clip With Model (bundled in Volume Clip extension)
Volume Clip With Roi (bundled in Volume Clip extension)
Volume Rendering (built-in)
Volumes (built-in)
Voting Binary Hole Filling Image Filter (built-in)
Welcome (built-in)
Window Level Effect (bundled in Window Level Effect extension)
Workflow Segmentation (bundled in Perk Tutor extension)
Xnat Slicer (bundled in XNATSlicer extension)

Modules by category

30 categories:

BRAINS
- Label Statistics
CMF Registration
- Voxelbase Registration
Converters
Developer Tools
- DICOM Plugins
- Editor Extensions
- Matlab
Diffusion
- Diffusion Data Conversion
- Diffusion Tensor Images
- Diffusion Weighted Images
- Tractography
Editor Effects
Endoscopy
Examples
Exporter
Filtering
- Arithmetic
- Denoising
- Morphology
IGT
Informatics
Legacy
- Converters
- Diffusion
  - Denoising
  - Diffusion Data Conversion
- Filtering
- Registration
- Work in Progress
  - Diffusion Tensor
    - Test
Mesh Generation
Mesh Generation
Microscopy
Multidimensional data
Multi Volume Support
Perk Tutor
Quantification
- Change Quantification
Registration
- Specialized
Segmentation
- Specialized
Slicelets
Surface Models
Testing
- Test Cases
Unspecified
Utilities
- BRAINS
Wizards
Work in Progress
- Converters
- Informatics
  - Test Cases
XNATSlicer

BRAINS

LabelStatistics

BRAINSLabel Stats (built-in)

CMF Registration

Apply Matrix (bundled in CMFreg extension) Landmark Registration (bundled in CMFreg extension) Surface Registration (bundled in CMFreg extension) Label Extraction (bundled in CMFreg extension) Label Addition (bundled in CMFreg extension) Downsize (bundled in CMFreg extension)

Voxelbase Registration

Growing (bundled in CMFreg extension) Mask Creation (bundled in CMFreg extension) Non Growing (bundled in CMFreg extension)

Converters

Vector To Scalar Volume (built-in) Crop Volume (built-in) Create DICOMSeries (built-in) Orient Scalar Volume (built-in)

Developer Tools

Event Broker Double Arrays (built-in) Py Dev Remote Debug (bundled in Py Dev Remote Debug extension) Cameras (built-in) Extension Wizard (built-in) Execution Model Tour (built-in) Image Maker (bundled in Image Maker extension)

DICOM Plugins

DICOMRWVMPlugin DICOMLongitudinal PETCTPlugin Multi Volume Importer Plugin DICOMPETSUVPlugin DICOMDiffusion Volume Plugin DICOMSegmentation Plugin DICOMScalar Volume Plugin DICOMSlicer Data Bundle Plugin

Editor Extensions

Binary Watershed Effect (bundled in IASEM extension) Fast Grow Cut Effect (bundled in Fast Grow Cut Effect extension) Carrera Slice Effect (bundled in Carrera Slice extension) Double Threshold Effect (bundled in IASEM extension)

Matlab

Matlab Module Generator (bundled in Matlab Bridge extension) Matlab Commander (bundled in Matlab Bridge extension)

Diffusion

Tractography Display (built-in) DICOM2Full Brain Tractography (built-in)

Diffusion Data Conversion

DWIConvert (built-in)

Diffusion Tensor Images

Resample DTIVolume (built-in) Diffusion Tensor Scalar Measurements (built-in) Tractography Label Map Seeding (built-in) Tractography Interactive Seeding (built-in)

Diffusion Weighted Images

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

Tractography

Fiber Bundle To Label Map (built-in) Fiber Bundle Label Select (built-in)

Editor Effects

Window Level Effect (bundled in Window Level Effect extension)

Endoscopy

Endoscopy (built-in)

Examples

Carrera Slice (bundled in Carrera Slice extension) Fast Grow Cut (bundled in Fast Grow Cut Effect extension) Fast Grow Cut Segmenter (bundled in Carrera Slice extension) Segmentation Aided Registration (bundled in Segmentation Aided Registration extension)

Exporter

Slicer To Kiwi Exporter (bundled in Slicer To Kiwi Exporter extension)

Filtering

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

IGT

Percutaneous Approach Analysis (bundled in Percutaneous Approach Analysis extension) Port Placement (bundled in Port Placement extension) Open IGTLink IF (built-in) Needle Finder (bundled in Needle Finder extension) Tracker Stabilizer (bundled in Tracker Stabilizer extension) Gyro Guide (bundled in Gyro Guide extension) i Gyne (bundled in i Gyne extension) Corner Annotation (bundled in Corner Annotation extension)

Informatics

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

Legacy

Converters

BSpline To Deformation Field (built-in)

Diffusion

Denoising

DWIUnbiased Non Local Means Filter (built-in)

Diffusion Data Conversion

DTIimport (built-in) DTIexport (built-in)

Filtering

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

Registration

Test Grid Transform Registration (built-in) Expert Automated Registration (built-in)

Work in Progress

Diffusion Tensor

Test

Diffusion Tensor Test (built-in)

Mesh Generation

Cleaver CLI (bundled in Cleaver Extension extension)

MeshGeneration

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

Microscopy

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

Multidimensional data

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

MultiVolume Support

Multi Volume Explorer (built-in) Multi Volume Importer (built-in)

Perk Tutor

Python Metrics Calculator (bundled in Perk Tutor extension) Workflow Segmentation (bundled in Perk Tutor extension) Transform Recorder (bundled in Perk Tutor extension) Perk Evaluator (bundled in Perk Tutor extension)

Quantification

PETStandard Uptake Value Computation (built-in) SUVFactor Calculator (bundled in PETDICOMExtension extension) Spinal Curvature Measurement (bundled in Scoliosis extension) Pk Modeling (bundled in Pk Modeling extension) Label Statistics (built-in) PETSUVImage Maker (bundled in Longitudinal PETCT extension) Dice Computation (bundled in Dice Computation extension) Data Probe (built-in)

ChangeQuantification

Intensity Difference Metric (bundled in Change Tracker extension)

Registration

BRAINSResample (built-in) Transforms (built-in) BRAINSResize (built-in) Perform Metric Test (built-in) BRAINSFit (built-in) PBNRR (bundled in PBNRR extension)

Specialized

ACPCTransform (built-in) Fiducial Registration (built-in) VBRAINSDemon Warp (built-in) BRAINSDemon Warp (built-in) Reformat (built-in)

Segmentation

Editor (built-in) EMSegment Quick (built-in) Simple Region Growing Segmentation (built-in) EMSegment (built-in) Volume Clip With Roi (bundled in Volume Clip extension) Swiss Skull Stripper (bundled in Swiss Skull Stripper extension) Airway Segmentation CLI (bundled in Airway Segmentation extension) LAScar Segmenter (bundled in LAScar Segmenter extension) Sobolev Segmenter (bundled in Sobolev Segmenter extension) Volume Clip With Model (bundled in Volume Clip extension) IGR3D MABMIS Testing (bundled in MABMIS extension) ABC (bundled in ABC extension) IGR3D MABMIS Training (bundled in MABMIS extension) Intensity Segmenter (bundled in Intensity Segmenter extension)

Specialized

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

Slicelets

Gel Dosimetry Analysis Algo (bundled in Gel Dosimetry Analysis extension)

Surface Models

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

Testing

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

TestCases

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

Unspecified

BRAINSDWICleanup (built-in)

Utilities

Thingiverse Browser (bundled in Thingiverse Browser extension) EMSegment Transform To New Format (built-in) Data Store (built-in)

BRAINS

BRAINSTransform Convert (built-in)

Wizards

Compare Volumes (bundled in CMFreg extension) Change Tracker (bundled in Change Tracker extension)

Work in Progress

Longitudinal PETCT (bundled in Longitudinal PETCT extension)

Converters

Label To DICOMSEGConverter (bundled in Reporting extension)

Informatics

Reporting (bundled in Reporting extension)

TestCases

Reporting Self Test Label To DICOMSEGConverter Self Test

XNATSlicer

Xnat Slicer (bundled in XNATSlicer extension)

Modules by contributing organization

62 contributing organizations:

Asclepios INRIA
AZE R&D
Brigham and Women's Hospital
BWH
BWH, SPL
BWH, SUMS
BWH/UAB
College of Information Engineering, Zhejiang University of Technology, Hangzhou, China); Xiaolei Chen, Jiashu Zhang(Department of Neurosurgery, PLA General Hospital, Beijing, China
CRTC
gatech
GE
Georgia Institute of Technology
Georgia Tech
IBM
Isomics
Isomics Inc.
Isomics, Inc.
Isomics, pieper@isomics.com
Kitware
Kitware)
MGH
Moka Creative, LLC, kumar.sunil.p@gmail.com
MSC/NLM
Noware
Orobix
Perk Lab at Queen's University
Perk Lab, Queen's
Perk Lab, Queen's University
PMH
Queen's
Queen's University
Radiation Medicine Program, Princess Margaret Hospital, University Health Network Toronto
SAIC-Frederick, NCI-Frederick
SBU
SCI Institute
Shiga University of Medical Science, Japan, SPL
SNR
SPL
SPL B&W Harvard
SPL, BWH
SPL, BWH, UPenn
Stony Brook University
SUMS
Surgical Planning Lab
UAB
Uiowa
UIowa
UNC
Univ of Michigan
Univ. of Iowa
University College Cork
University of Alabama Birmingham
University of Heidelberg
University of Iowa
University of Iowa) and Andrey Fedorov (SPL
UPenn
Utah
UVa
UWA
Wash U-St. Louis, dmarcus@wustl.edu
while at GE

Asclepios INRIA

PBNRR (bundled in PBNRR extension)

AZE R&D

JRC2013Vis

Brigham and Women's Hospital

Corner Annotation (bundled in Corner Annotation extension)
Surface Toolbox (built-in)
test tractography display

BWH

Add Many Markups Fiducial Test
Change Tracker Self Test
Colors Scalar Bar Self Test
Curve Maker (bundled in Curve Maker extension)
Dice Computation (bundled in Dice Computation extension)
DICOMRWVMPlugin
Fast Grow Cut Effect (bundled in Fast Grow Cut Effect extension)
Fiducial Layout Switch Bug1914
Markups (built-in)
Markups In Compare Viewers Self Test
Markups In Views Self Test
Neurosurgical Planning Tutorial Markups Self Test
Segmentation Aided Registration (bundled in Segmentation Aided Registration extension)
Volume Rendering Scene Close (built-in)
Window Level Effect (bundled in Window Level Effect extension)