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asl-preprocessing

Workflow to obtain ASLPrep output

  1. Run fMRIPrep

    • ASLprep reuses the anatomical derivatives from fMRIPrep output
  2. Create a new dataset of fMRIPrep output using Datalad

    • Run datalad install to make a copy of the fMRIPrep output: code/datalad_install_dataset.sh
    • Rename files and modify folder hierarchy: code/datalad_rename_dataset.sh
      • datalad unlock the dataset
      • Run rename.ul
      • datalad save the changes
  3. Run ASLprep

    • Create a json file describing custom BIDS input filters: code/aslprep_filter.json
      • To only include baseline T1w and ASL scans
    • Run the bash script: code/run_tay_aslprep.sh
      • Submit SLURM jobs
      • Use output spaces MNI152NLin2009cAsym and asl
      • Set --smooth_kernel to 0
      • Set --m0_scale to 100
      • Include --bids-filter-file, --anat-derivatives, [--skip_bids_validation
  4. QC ASLprep output

    • QC file: sub-CMH*/ses-01/perf/*desc-quality_control_cbf.csv
  5. Run statsitical analysis

    • Havard Oxford atlas: sub-CMH*/ses-01/perf/*desc-HavardOxford_mean_cbf.csv

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Ghazaleh Ahmadzadeh

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