sbatch_fmriprep.sh

#!/bin/bash

# Add your SLURM options here
#SBATCH --mail-type=ALL 			# Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=oliver.mcneil@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=4
#SBATCH --mem=16gb
#SBATCH --time=08:00:00				# 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

# Add commands needed to run fmriprep

SUBJECT = $1

module load singularity

singularity run --cleanenv \
--bind /scratch/psyc5171/exercises/mbdata/bids:/data \
--bind /scratch/ham19006/hw5/results:/out \
/scratch/psyc5171/containers/fmriprep_1.5.9.sif \
--nthreads 4 --omp-nthreads 4 \
--fs-license-file /data/code/license.txt \
--cifti-output \
/data /out participant

# NOTE: For FSL license file, can put command after /data binding and use /data/code/license.txt instead