CCB Automated Volume Calculation of 56 ROIs Workflow

Overview - Automated 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
  • 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

Pipeline Workflows

• PNG Image of the Validated Pipeline Workflow .
• Automated_56ROI_VolumeParsing.pipe (11/03/2009)

Footnotes

• Outputs and results: tabular results are Nx56 matrices, where N=#-subjects for all 56 ROIs.
• Expected times: about 3 hrs.
• Limitations: For some data/populations, the pre-processing steps (skull-stripping, tissue segmentation, etc.) may need to be improved/replaced by analogous processes (e.g., SSMA for Skull-stripping).
• Contact person/group: SIG-FLOW Team
• Pubs: Publications
• Grants: U54 RR021813, P41 RR013642
• Tools/packages used in this workflow: BrainSuite, FSL, ITK, CCB tools.
• Notes: Mature