#!/bin/bash
#SBATCH --mail-type=BEGIN,END,FAIL		# Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=willibwe@bc.edu		# Your email address
#SBATCH --nodes=1				# OpenMP requires a single node
#SBATCH --ntasks=4				# Run 4 serial tasks
#SBATCH --mem=20gb
#SBATCH --time=36:00:00				# Time limit hh:mm:ss
#SBATCH -e error_%A_%a.log			# Standard error
#SBATCH -o output_%A_%a.log			# Standard output
#SBATCH --job-name=fmriprep			# Descriptive job name

##### END OF JOB DEFINITION  #####

# Written by SEW 11/30/21; Edited for fmriprep 12/16/21.
# Purpose: Run fmriprep (preprocessing) for the memory task for each participant specified in CogNeuro_IDs.txt. Currently runs one participants at a time as of 12/16/21.
# Usage: Run from [/mmfs1/data/kensinel/canlab/cogneuro/bids]$ sbatch sbatch_fmriprep.sh CogNeuro_IDs.txt

filename="$1"

while read -r line; 

do 

module load singularity
singularity run --cleanenv \
--bind /mmfs1/data/willibwe/work2:/work \
--bind /mmfs1/data/kensinel/canlab/cogneuro/bids:/data \
--bind /mmfs1/data/kensinel/canlab/cogneuro/bids/derivatives/fmriprep:/out \
/mmfs1/data/willibwe/fmriprep_21.0.0_test.simg \
/data /out participant \
--participant_label $line -w /work \
--skip_bids_validation \
--task-id HRTASK \
--nprocs 1 --omp-nthreads 1 \
-vvv \
--ignore t2w flair \
--output-spaces MNI152NLin2009cAsym \
--bold2t1w-init register \
--bold2t1w-dof 6 \
--dummy-scans 5 \
--random-seed 0 \
--return-all-components \
--fd-spike-threshold 0.9 \
--skull-strip-template OASIS30ANTs \
--skull-strip-fixed-seed \
--skull-strip-t1w auto \
--fs-license-file /data/license.txt \
--resource-monitor

mv error*.log derivatives/fmriprep/logs/
mv output*.log derivatives/fmriprep/logs/

done < "$filename"