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