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.

Building BRAINS

• Building BRAINS - brains:Building
• Installation - brains:Installation
• Configuring - brains:Configure

Environment Setup

• Setup Environment - brains:Environment

Included Tools

Core

• brains3 - brains:CommandLine
  1. Setup Environment - brains:Environment
  2. Scripting
     • Convenient Commands - brains:Scripting Help
     • ITK TCL Wrapping - brains:ITK Scripting
     • BRAINS Wrapping - brains:Wrapping
     • BRAINS Namespaces - brains:Namespaces
  3. 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