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fmriprep.sh
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fmriprep.sh
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#!/bin/bash
#SBATCH --time=13:00:00
#SBATCH --account=def-afyshe-ab
#SBATCH -n 1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=32G
#SBATCH --mail-user=jam10@ualberta.ca
#SBATCH --mail-type=BEGIN
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=REQUEUE
#SBATCH --mail-type=ALL
cd
module load apptainer
project=~/projects/def-afyshe-ab/jamesmck/bird_data_analysis
sub_num="29"
cp -r ${project}/data/raw_data $SLURM_TMPDIR/
# Create directories for fMRIprep to access at runtime
mkdir $SLURM_TMPDIR/work_dir
mkdir $SLURM_TMPDIR/sub_${sub_num}_out
mkdir $SLURM_TMPDIR/image
mkdir $SLURM_TMPDIR/license
# Required fMRIprep files
cp ${project}/fmriprep_24.0.0.sif $SLURM_TMPDIR/image
cp ${project}/license.txt $SLURM_TMPDIR/license
apptainer run --cleanenv \
-B $SLURM_TMPDIR/raw_data/results/TC2See:/raw \ # Input data. Should contain one folder per participant ("sub-01").
-B $SLURM_TMPDIR/sub_${sub_num}_out:/output \ # Output location.
-B $SLURM_TMPDIR/work_dir:/work_dir \
-B $SLURM_TMPDIR/image:/image \
-B $SLURM_TMPDIR/license:/license \
$SLURM_TMPDIR/image/fmriprep_24.0.0.sif \
/raw /output participant \
--participant-label ${sub_num} \
--work-dir /work_dir \
--fs-license-file /license/license.txt \
--output-spaces fsaverage \ # Change to appropriate output space.
--stop-on-first-crash
# Zip processed output
tar -czf $SLURM_TMPDIR/sub_${sub_num}_out.tar.gz -C $SLURM_TMPDIR sub_${sub_num}_out
# Copy back to project
cp $SLURM_TMPDIR/sub_${sub_num}_out.tar.gz ${project}/data/processed/