sbatch_fmriprep.sh

#!/bin/bash
#SBATCH --mail-type=ALL 			# Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=Shaun.James@uconn.edu	# Your email address
#SBATCH --nodes=1					# OpenMP requires a single node
#SBATCH --ntasks=1					# Run a single serial task
#SBATCH --cpus-per-task=8
#SBATCH --mem=48gb
#SBATCH --time=48:00:00				# 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
#SBATCH --partition=serial            # Use a serial partition 24 cores/7days
##### END OF JOB DEFINITION #####

SUBJECT=$1

module load singularity

singularity run --cleanenv \
--bind /scratch/shj16108/hw5/hw5/bids:/data \
--bind /scratch/shj16108/hw5/hw5/fmriprepo:/out \
/scratch/psyc5171/containers/fmriprep_1.5.9.sif \
--participant_label 01 \
--nthreads $SLURM_CPUS_PER_TASK --omp-nthreads $SLURM_CPUS_PER_TASK
--fs-license-file /data/code/license.txt \
--cifti-output \
--use-syn-sdc --use-aroma \
/data /out participant