Downloading PCX MRI Data from Flywheel

Downloading BIDS Data

  1. Log into Amarel Note– to do this you must have flywheel setup in your command line. Follow these instructions to setup the legacy command line: https://holmeslab.github.io/holmeslab/docs/Experiments/flywheel-cli/
  2. In terminal or the Amarel OnDemand GUI, navigate to this file: /projects/f_ah1491_1/analysis_tools/flywheel/bids_download/download_bids_PCX_Joss.ipynb
  3. Modify parameters to specify which subjects you would like to download from
  4. Run the notebook, which will do these things:
    1. Create a new slurm shell script for each subject, with the slurm header and the bash command to download that subject’s bids file
      • Specifying subject-specific .err and .out files
    2. Send the script to slurm as a job
  5. Check

Downloading fMRIPrep Data

  1. Log into Amarel
  2. In terminal or the Amarel OnDemand GUI, navigate to this file: /projects/f_ah1491_1/analysis_tools/flywheel/fmriprep_download/download_fmriprep_PCX.ipynb
  3. Make a copy to modify for your needs (ie specifying which data types, which data files, which subjects, which sessions, etc. you would like to download). If you run this script, it will submit a slurm job to download all subjects.
  4. Check the download succeeded by looking for your files in /scratch/f_ah1491_1/internal_data/PCX/derivatives/fmriprep