#!/bin/bash


#SBATCH -p sapphire
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=3
#SBATCH --time=20:00:00
#SBATCH --mem=100G
#SBATCH -o ME_%A_%a_output.out
#SBATCH -e ME_%A_%a_error.out
#SBATCH --job-name=ME_fmriprep

myproject='/data/scratch/projects/'


date
echo $myproject
echo $SLURM_JOB_NAME
echo $SLURM_ARRAY_TASK_ID

module load GCC
module load Apptainer


SUBJECT=`sed -n -e "${SLURM_ARRAY_TASK_ID}p" ${myproject}/ME_no_fieldmap/sublist.txt`

echo "subject number: " ${SUBJECT}


# launch processing for each subject

export APPTAINERENV_TEMPLATEFLOW_HOME="$HOME/.cache/templateflow"  # Tell fMRIPrep the mount point

apptainer run -B "${myproject}":"${myproject}" --cleanenv "${myproject}/fmriprep-25.0.simg" --skip-bids-validation "${myproject}/ME_no_fieldmap" "${myproject}/ME_no_fieldmap_processed" --low-mem participant --participant-label "${SUBJECT}" --fs-license-file "${myproject}/license.txt" --output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-2 --stop-on-first-crash --me-output-echos -w /tmp/