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levin-stroke

Get data into BIDS format

Download dcm2bids and run (for one subject):

dcm2bids -d <PATH_TO_DICOM> -p sub-<ID> -c config_levin-stroke.txt

Where <ID> is the subject ID, eg: 007PGA

The BIDS dataset is stored privately under git-annex/datasets/levin-stroke

Process data

Processing pipeline for project involving stroke patients. PI is Dr. Levin.

The processing pipeline outputs the following metrics:

  • Cord cross-sectional area at C2/C3 vertebral level
  • DTI metrics & MTR, MTsat within white matter tracts: R/L CST, dorsal column, R/L RST

The processing pipeline uses the following images:

  • T2w
  • DWI
  • GRE with/without MT pulse

The main steps involve:

  • QC data for artifacts
  • Curate data for BIDS compliance
  • Run analysis script (which relies on SCT).
  • QC analysis, manual correction of spinal cord masks and vertebral labeling
  • Re-run analysis with corrected masks
  • Aggregate results into CSV file

How to use:

pip install -r requirements.txt
sct_run_batch -jobs -1 -path-data ~/data/levin-stroke -path-output ~/levin_results/ -script ~/code/levin-stroke/process_data.sh

Results

Results are available in releases: https://github.com/sct-pipeline/levin-stroke/releases