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HCPPipelines Tutorial

Data

Organize your data into BIDS format

bids/
├── dataset_description.json
└── sub-001
    └── anat
        ├── sub-001_T1w.json
        ├── sub-001_T1w.nii
        ├── sub-001_T2w.json
        └── sub-001_T2w.nii

Script

Save the following sbatch script as hcppipeline.sh. Edit the paths to the BIDS folder and outputs.

#!/bin/bash

set -u

export TMPDIR=/ssd/home/$USER/TEMP
participant_label=$1

# The --license_key is supposedly for freesurfer, but I don't think it's actually used...
podman run --rm \
  -v "$HOME":"$HOME" \
  docker.io/bids/hcppipelines:v4.3.0-3 \
    "$HOME"/path/to/bids/ "$HOME"/path/to/outputs participant \
    --participant_label "$participant_label" \
    --license_key idk \
    --stages PreFreeSurfer FreeSurfer PostFreeSurfer

Run

To run participant sub-001, pass the script and participant label to sbatch from the head node of the HPC

sbatch hcppipeline.sh 001