brains:MainPage
From NITRC Wiki
The BRAINS software suite is focused on the analysis of morphometric MR images to study brain changes associated with Psychiatric and Neurological disorders. There is both a command line tool and a graphical user interface (GUI) as well as several command line programs. The command line is based on TCL and provides access the ITK libraries allowing custom pipelines to be developed. Documentation for each component is provided in the following sections.
Contents |
Building BRAINS
- Building BRAINS - brains:Building
- Installation - brains:Installation
- Configuring - brains:Configure
Environment Setup
- Setup Environment - brains:Environment
Included Tools
Core
- brains3 - brains:CommandLine
- Setup Environment - brains:Environment
- Scripting
- Convenient Commands - brains:Scripting Help
- ITK TCL Wrapping - brains:ITK Scripting
- BRAINS Wrapping - brains:Wrapping
- BRAINS Namespaces - brains:Namespaces
- AutoWorkup
- Running - brains:Autoworkup
- Algorithm - brains:WorkupAlgorithm
- Measurements - brains:WorkupMeasurements
- BRAINSTracerQt - brains:BRAINSTracer
Registration
- BRAINSFit - multimodereg:MainPage
- BRAINSDemonsWarp - brainsdemonwarp:MainPage
- BRAINSConstellationDetector - brainscdetector:MainPage
- BRAINSResample
Tissue Classification
- BRAINSClassPlugs - brains:BRAINSClassPlugs
- BRAINSClassify - brains:BRAINSClassify
- BRAINSDiscreteClass - brains:BRAINSDiscreteClass
- BRAINSKmeansClusterSamples - brains:BRAINSKmeansClusterSamples
- BayesianClassifier - brains:BayesianClassifier
- BRAINSABC
Automated Labeling
- BRAINSMush - BRAINSMush
- SkullStripper - Slicer Skull Stripper
- BRAINSTalairach - brains:BRAINSTalairach
- BRAINSTalairachMask - brains:BRAINSTalairachMask
- BRAINSCut
Surface Analysis
- GenusZeroImageFilter - brains:GenusZeroImageFilter
- BRAINSSurfaceGeneration - brains:BRAINSSurfaceGeneration
- BRAINSApplySurfaceLabels - brains:BRAINSApplySurfaceLabels
- BRAINSMeasureSurface - brains:BRAINSMeasureSurface
- BRAINSAssignSurfaceFeatures - brains:BRAINSAssignSurfaceFeatures
- BRAINSSurfaceFlattening - brains:BRAINSSurfaceFlattening
- BRAINSSurfaceRegistration - brains:BRAINSSurfaceRegistration
Diffusion Tensor Analysis
- GTRACT
- DTIPrep - dtiprep:MainPage
Other
- N4ITK - brains:N4ITK
Tasks
- Removing OrientImageFilter - brains:RemoveOrientImageFilter








