Flywheel fMRIPrep Tutorial

Flywheel: https://cahbir-flywheel.rutgers.edu/#/projects

TABLE OF CONTENTS:

Tutorial: Flywheel BIDS to fMRIPrep process

  1. ‘Run gear’
  2. ‘Run analysis gear’
    • NOT ‘fMRIPREP: A robust…”
    • Select “BIDS Apps: BIDS fMRIPrep” to run
  3. Input
    • Add in your FreeSurfer license file freesurfer_license_jun2024.txt
      • way1: copy contents of text file > configuration > ‘gear FREESURFER LICENSE’
      • way2: Information > Attachments > Attach freesurfer license .txt
      • way3: Information > Custom Information > ‘+’ called FREESURFER_LICENSE > copy paste the .txt file into there
  4. Job Tags: ‘extra-large’
  5. Configuration -
    • most recent is 1.5.1_24.0.0, but can choose your version
    • bids_app_command for PCR:

bids_app_command for PCR:

fmriprep bids_dir output --no-submm-recon --bold2anat-dof 6 --output-spaces T1w fsnative fsaverage MNI152NLin2009cAsym:res-native MNI152NLin2009cAsym:res-2 --cifti-output 91k --write-graph

  1. Finally, press ‘Run Gear’

    Wait 12-24 hours

Getting fMRIPrep to work on Flywheel

If you need to check error log, you can download it here:

image.png