README.md

1. Weekly participant recruitment stats weekly_report.py
2. Download XNAT, then convert to BIDS using dcm2bids detailing in bids_conversion.sh. This bash script also calls 2 python scripts:
   • xnat_download.py: Download DICOM from XNAT
   • modify_json.py: Edit JSON file according to BIDS conventions
3. Running MRIQC and fMRIPrep locally using docker, steps detailed in MRIQC_fMRIPrep.ipynb
4. Running MRIQC on Flywheel
   • Setting up Flywheel CLI: Flywheel.ipynb
   • Importing BIDS-formatted data to Flywheel, then run the MRIQC gear flywheel_import_mriqc.sh.
     • This bash script calls flywheel_mriqc.py to run MRIQC gear on Flywheel for specified subject and scan type (anat or func - also, which func task).
5. Exploratory test if brain volumes (Freesurfer T1w) and immune markers can be used to predict drug use and childhood trauma.
6. Resting State: Work in progress