Automated Brain Tissue Extraction and Volume Calculation Workflow

This workflow takes raw un-skull-stripped volumes and generates tables of the volumes for all 56 ROIs currently automatically extracted using LONI BrainParser.

Problem addressed by this workflow

Computing and tabulating the Brain Volumes of 56 cortical and sub-cortical ROIs. This workflow also generates DX models of all 56 ROIs which can be viewed as a scene in ShapeViewer.

Detailed Workflow Usage & Specifications

• Input: Any volumetric file format can be used for the raw unskull-stripped imput images (e.g., DICOM, DIrectories, Analyze, MNC, Nifti, etc.)
• Pre-processing
  • Image conversion to Analyze
  • Converting to 8-bit
  • Intensity Inhomogeneity correction
  • Skull-stripping (use either BET:AutoROI_Extraction workflow or with SSMA:AutoROI_Extraction_V2 workflow)
  • Affine Registration
• Auto Volume Parsing
  • Non-linear Registration to LPBA40 Atlas
  • 56 ROI Volume Parcellation
  • Mapping of ROI labels in native space
• Compute the 56 ROI regional brain volumes
• Tabulate the Volumetric data across subjects

URL: http://www.loni.ucla.edu/twiki/bin/view/CCB/PipelineWorkflows_56ROI_BrainVolumes

Try this Pipeline workflow online now!