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hw7/fmriprep.sh
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#!/bin/bash | |
#SBATCH --mail-type=ALL # Mail events (NONE, BEGIN, END, FAIL, ALL) | |
#SBATCH --mail-user=aliyar.ozercan@uconn.edu | |
#SBATCH --nodes=1 # OpenMP requires a single node | |
#SBATCH --ntasks=1 # Run a single serial task | |
#SBATCH --cpus-per-task=16 | |
#SBATCH --mem=48gb | |
#SBATCH --time=72:00:00 # Time limit hh:mm:ss | |
#SBATCH -e error_%A_%a.log # Standard error | |
#SBATCH -o output_%A_%a.log # Standard output | |
#SBATCH --job-name=fmriprep2 # Descriptive job name | |
#SBATCH --partition=serial # Use a serial partition 24 cores/7days | |
##### END OF JOB DEFINITION ##### | |
SUBJECT=$5 | |
module load singularity | |
singularity run --cleanenv \ | |
--bind /scratch/psyc5171/alo18003/final19/bids:/data --bind /scratch/psyc5171/alo18003/final19/output:/out \ | |
/scratch/psyc5171/containers/fmriprep_1.5.9.sif \ | |
--participant_label NDARAA948VFH NDARAC853DTE NDARAG340ERT NDARAH948UF0 NDARAM675UR8 \ | |
--nthreads $SLURM_CPUS_PER_TASK --omp-nthreads $SLURM_CPUS_PER_TASK \ | |
--fs-license-file license.txt \ | |
/data /out participant |