End to end pipeline for processing neonatal MRI data for CMRO2 calculations
The pipeline will organize raw DICOM data into the BIDS format, run the dHCP pipeline, create inidividual tissue masks, process SWI/R2*, and process ASL and QSM data
Prior to running the pipeline, there are a number of dependencies that will need to be installed and set-up
The following github repos will also need to be downloaded
At the beginning of the pipeline, change the paths of the following variables in pipeline.sh to their respective directory:
$maindir, $qsmscript, $juliascript, $cbfscript, $cbftissue_script
The pipeline takes in a TSV file with 11 variables and will output another TSV file with 30 variables
TSV input file requirements include Subject ID, PMA, DICOM folder numbers for T1W, T2W, ASL, DTI Blip-up, DTI Blip-down, and QSM scans, HCT value, CSaO2 value, and thread number
cd into the directory with the pipeline and run the pipeline using the following code
./pipeline.sh -f /full/path/of/input/tsv/file