run fmriprep in multiple tmux sessions in parallel

run_tmux_fmriprep.sh

#!/bin/bash
# NOTE: make sure freesurfer licence is under ${HOME}/.freesurfer.txt before running the script
SING_IMG="/data/cisl/containers/fmriprep-20.2.1lts.sif"
DATASET="ds000228"
DATASET_DIR="/data/cisl/datasets/${DATASET}"

# run BIDS validator
singularity exec -B ${DATASET_DIR}/${DATASET}_openfmri:/DATA \
    ${SING_IMG} bids-validator \
    /DATA

SUBJECTS_LIST=($(ls ${DATASET_DIR}/${DATASET}_openfmri/sub-* -d))
N_SUBJECTS=10 

for i in $(seq ${N_SUBJECTS}); do
    i=$((i-1))
    subject=${SUBJECTS_LIST[$i]}
    participant_id=${subject#*-}

    # create fmriprep command
    FMRIPREP_CMD=$(cat << CMD
export SINGULARITYENV_FS_LICENSE=${HOME}/.freesurfer.txt
singularity run --cleanenv -B ${DATASET_DIR}:/WORK -B ${HOME}/.cache/templateflow:/templateflow -B /etc/pki:/etc/pki/ \
    ${SING_IMG} \
    -w /WORK/fmriprep_work \
    --output-spaces MNI152NLin2009cAsym MNI152NLin6Asym \
    --notrack --write-graph --resource-monitor \
    --omp-nthreads 1 --nprocs 1 --mem_mb 65536 \
    --fs-license-file /WORK/freesurfer.txt \
    --participant-label ${participant_id} --random-seed 0 --skull-strip-fixed-seed \
    /WORK/${DATASET}_openfmri /WORK/derivatives participant &   # create detached session
CMD
)
    # send to a tmux session
    tmux new -d -s sub-${participant_id}
    tmux send-keys -t sub-${participant_id}.0 "$FMRIPREP_CMD" ENTER
done

# quick check of console output
# tmux capture-pane -S -100 -pt sub-001