run

#!/bin/bash
#SBATCH -J spacetop-fmriprep
#SBATCH -o logs/%a.log
#SBATCH -t 16:00:00
#SBATCH -p normal
#SBATCH -N 1 -n 1
#SBATCH -A A2CPS

PS4='+ $(date) '
set -uex

ROOT="${SLURM_SUBMIT_DIR}"
IMAGE=code/containers/fmriprep_25_1_4.sif
SOURCEDATA="${ROOT}"/sourcedata
RAWDATA="${SOURCEDATA}"/raw

if ((SLURM_ARRAY_TASK_ID > 116)); then
    printf "The Slurm array ID is too high. There are only 117 participants [IDs: 0-116].\n" >&2
    exit 1
fi

mapfile -t subs < <(find "${RAWDATA}" -mindepth 1 -maxdepth 1 -type d -name "sub-*" | sort | grep -oP "(?<=sub-)[0-9]+")
participant_label="${subs[${SLURM_ARRAY_TASK_ID}]}"


apptainer run \
    --bind "${ROOT}" \
    --env TEMPLATEFLOW_HOME="${SOURCEDATA}"/templateflow \
    ${IMAGE} \
    --fs-license "${ROOT}"/code/license \
    --participant-label "${participant_label}" \
    --skip-bids-validation \
    --ignore slicetiming \
    --dummy-scans 6 \
    --cifti-output 91k \
    --mem 100000 \
    -w ${SCRATCH}/work \
    sourcedata/raw "${ROOT}" participant