mri2mesh.sh

#!/bin/bash
#SBATCH --partition=high-moby
#SBATCH --nodes=1
#SBATCH --cpus-per-task=6
#SBATCH --mem-per-cpu=2G
#SBATCH --time=30:00:00
#SBATCH --export=ALL
#SBATCH --job-name="mri2mesh"
#SBATCH --output=/projects/ttan/UBC-TMS/simnibs/code/logs/mri2mesh_UBC-TMS_60k_vertices_new_subjects_%j.txt
#SBATCH --array=1-2

module load FSL/6.0.1
module load freesurfer/6.0.1

export SUBJECTS_DIR=/projects/ttan/UBC-TMS/simnibs/mri2mesh
study="UBC-TMS"
sublist=/projects/ttan/${study}/simnibs/rerun_sublist_v01.txt
indir=/projects/ttan/${study}/simnibs/anat
outdir=/projects/ttan/${study}/simnibs/mri2mesh

#mkdir ${outdir}

index() {
   head -n $SLURM_ARRAY_TASK_ID $sublist \
   | tail -n 1
}

sub_f=$(find ${indir}/ -type f -name "`index`_*T1w.nii.gz")

cd ${outdir}
mri2mesh --all `index` $sub_f

# This is how you run pipelines in the tmp directory in kimel lab insteadl of NFS
#tmp_dir=$(mktemp -d "/tmp/mri2mesh.XXXX")
#cd ${tmp_dir}
#ln -s $sub_f .
#cd ${outdir}

#mri2mesh --all `index` $(basename $sub_f)
#mv m2m* $outdir
#mv fs* $outdir