sbatch_mriqc.sh

#!/bin/bash
##### Job definition
#SBATCH --nodes=1                                       # OpenMP requires a sin$
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --mem=8gb                                      # Run a single serial t$
#SBATCH --time=02:00:00                         # Time limit hh:mm:ss
#SBATCH -e mriqc_error_%A_%a.log                        # Standard error
#SBATCH -o mriqc_output_%A_%a.log                       # Standard output
#SBATCH --job-name=mriqc                     # Descriptive job name
#SBATCH --partition=serial

##### load required modules

module load singularity

# Add commands needed to run mriqc
singularity run --cleanenv \
      --bind /scratch/shj16108/hw3try2/hw3/bids:/data \
      --bind /scratch/shj16108/hw3try2/hw3/mriqc_output:/out \
      /scratch/psyc5171/containers/mriqc_latest.sif \
      /data /out participant \
      --nprocs 3