#!/bin/bash
#SBATCH -J fmriprep
#SBATCH --time=10:00:00
#SBATCH -n 1
#SBATCH --account=ctb-villens
#SBATCH --cpus-per-task=3
#SBATCH --mem-per-cpu=4G
#SBATCH --mail-user=****
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=REQUEUE
#SBATCH --mail-type=ALL

# Load singularity module
SINGULARITY_IMG="/project/ctb-villens/quarantine/Core/fmriprep/22.0.0/fmriprep-22.0.0.simg"
module load VilleneuveLab
module load singularity/3.8

# Allocate your input and output directories, and allocate local scratch as the working directory
WORK_DIR=$(mktemp -d -p "${SLURM_TMPDIR}" work_dir-XXXX) || exit 1
echo "working directory is $work_dir"/project/ctb-villens/dataset/PreventAD_2019-2020/mri/bids/

# Define path for TSV file
STUDY="/home/javan/scratch/multi_prep/test/script/me/version"

# Designate the location of your templateflow templates
export SINGULARITYENV_TEMPLATEFLOW_HOME=/project/ctb-villens/javan/templateflow
TEMPLATEFLOW_HOME="/project/ctb-villens/javan/templateflow"
export SINGULARITYENV_FS_LICENSE=/project/ctb-villens/quarantine/Core/freesurfer/6.0.0/license.txt
FS_LICENSE="/project/ctb-villens/quarantine/Core/freesurfer/6.0.0/license.txt"
#Parse the participants.tsv file and extract one subject ID from the line corresponding to this SLURM task
# The $((${SLURM_ARRAY_TASK_ID} + 1)) section is responsible for scipping the first line of the  participant tsv file

SUBJECT=$( sed -n -E "$((${SLURM_ARRAY_TASK_ID} + 1))s/sub-(\S*)\>.*/\1/gp" ${STUDY}/participants_all_NAV2_id.tsv )
BOLDPATH=$( sed -n -E "$((${SLURM_ARRAY_TASK_ID} + 1))s/sub-(\S*)\>.*/\1/gp" ${STUDY}/participants_all_NAV2_ses.tsv )

# Build your command to tell singularity to run fmriprep, ensuring it binds to your template directory, your scratch folder
SINGULARITY_CMD="singularity run --cleanenv \
 -B ${TEMPLATEFLOW_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME} \
 -B ${FS_LICENSE}:${SINGULARITYENV_FS_LICENSE} \
 -B /project/ctb-villens/dataset/PreventAD_2019-2020/mri/bids/sub-${SUBJECT}/ses-${BOLDPATH}/:/source_bids:ro \
 -B /home/javan/scratch/multi_prep/test/derivatives_me:/out \
 -B "${WORK_DIR}":/work \
 ${SINGULARITY_IMG} \
 /source_bids /out \
 participant --participant-label ${SUBJECT} \
 -w /work -vv --nthreads ${SLURM_CPUS_PER_TASK} \
 --mem_mb $((${SLURM_MEM_PER_CPU}*${SLURM_CPUS_PER_TASK}-256)) \
 --fs-license-file ${FS_LICENSE} \
 --skip_bids_validation \
 --output-spaces MNI152NLin2009cAsym:res-2 MNI152NLin2009cAsym anat \
 --fs-no-reconall --notrack"

# Setup done, run the command
echo Running task ${SLURM_ARRAY_TASK_ID}
echo Commandline: ${SINGULARITY_CMD}
eval ${SINGULARITY_CMD}
exitcode=$?

# Output results to a table
echo "sub-$subject   ${SLURM_ARRAY_TASK_ID}    $exitcode" \
              >> ${SLURM_JOB_NAME}.${SLURM_ARRAY_JOB_ID}.tsv
echo Finished tasks ${SLURM_ARRAY_TASK_ID} with exit code $exitcode
exit $exitcode