#!/bin/bash


#
## Slurm Setup
#
#SBATCH --job-name="recon-all-slurm"
#SBATCH --account=csd855
#SBATCH --partition=shared
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --time=48:00:00
#SBATCH --output="recon-all-slurm.%j.%N.out"
#SBATCH --error="recon-all-slurm.%j.%N.err"
#SBATCH --export=ALL
#SBATCH --mem=16G
#SBATCH --ntasks-per-node=8
#SBATCH --constraint="lustre"
export SLURM_EXPORT_ENV=ALL


#
# Arguments
#
if [ "$#" -ne 1 ]; then  # if the number of arguments is not equal to 1, then fail with usage
echo "
USAGE:  recon-all-slurm.sb image
e.g. recon-all-slurm.sb subjectfolder/test_image.nii
"
exit
else
echo "Now processing recon-all for subject $1"  # the first argument is $1
fi


#
## Command Setup
#
subject=`basename $1 | sed -e 's/\.[^.]*$//'`
filepath=`dirname $1`



#
## Environment
#
echo ""
echo "** Loading EXPANSE modules"
module purge
module load slurm
module load cpu/0.15.4
module load freesurfer
export SUBJECTS_DIR=$(cd "$(dirname $1)"; pwd)

echo ""
echo "** Processing:"
echo "SUBJECTS_DIR: $SUBJECTS_DIR"
echo "Subject:      $subject"
echo "File path:    $filepath"
echo "Command:      recon-all -s $subject -i $1 -fill -debug"

recon-all -s $subject -i $1 -fill -debug

mv "recon-all-slurm.%j.%N.out" $SUBJECTS_DIR 
mv "recon-all-slurm.%j.%N.err" $SUBJECTS_DIR