CCB Automated Tissue Extraction and Volume Calculation Workflow
Overview - Automated Tissue Extraction and Volume Calculation Workflow
This workflow takes raw un-skull-stripped volumes and generates tables of the total, GM, WM and CSF volumes.
Problem addressed by this workflow
Computing and tabulating the total Brain Volume (TBV), Gray-matter (GM), White-matter (WM) and CSF volumes for a collection of subjects.
Detailed Workflow Usage & Specifications
- Any volumetric file format can be used for the raw unskull-stripped imput images (e.g., DICOM, DIrectories, Analyze, MNC, Nifti, etc.)
- Image conversion to Analyze
- Skull-stripping
- Intensity Inhomogeneity correction
- Volume Tissue Classification
- Compute the Total, GM, WM and CSF brain volumes
- Tabulate the Volumetric data for all tissue types and across subjects
- Export the final volumetric table.
Pipeline Workflows
Footnotes
- Outputs and results: tabular results are Nx4 matrices, where N=#-subjects and 4 are the 4 tissue types
- Expected times: about 30 minutes.
- 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, CCB tools.
- Notes: Mature
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