#!/bin/bash
jobs=/data/scratch/kecannon/brainhack2018/jobs3_HCP
sub_dir=/data/scratch/kecannon/brainhack2018/HCP
mkdir $jobs

cd $sub_dir

for sub in `find * -type d`
do

#Create job script files
cat > $jobs/segment_$sub.sh <<EOF
#!/bin/bash

module load rc/matlab/R2013a
matlab -nodesktop -nosplash -r "cheaha_vessels_segment('$sub_dir','$sub')"

EOF
done

for sub in `find * -type d`
do

#Submit jobs
pushd $jobs
echo "submitting segment job for $sub"
sbatch --job-name=segment_$sub --output=segment_$sub.txt --ntasks=1 --partition=short --mem-per-cpu=9192 --time=12:00:00 segment_$sub.sh 
popd

done