Change job parameters to ask for more RAM and less compute time. Run for all subjects.

cheaha_vessels_segment.sh

 #!/bin/bash
-jobs=/data/scratch/kecannon/brainhack2018/jobs1_HCP
+jobs=/data/scratch/kecannon/brainhack2018/jobs2_HCP
 sub_dir=/data/scratch/kecannon/brainhack2018/HCP
 mkdir $jobs
 
 cd $sub_dir
 
-for sub in `find 99* -type d`
-#Test with 6 folders
+for sub in `find * -type d`
 do
 
 #Create job script files
@@ -19,14 +18,13 @@ matlab -nodesktop -nosplash -r "cheaha_vessels_segment('$sub_dir','$sub')"
 EOF
 done
 
-for sub in `find 99* -type d`
-#Test with 6 folders
+for sub in `find * -type d`
 do
 
 #Submit jobs
 pushd $jobs
 echo "submitting segment job for $sub"
-sbatch --job-name=segment_$sub --output=segment_$sub.txt --ntasks=1 --partition=long --mem-per-cpu=4096 --time=150:00:00 segment_$sub.sh 
+sbatch --job-name=segment_$sub --output=segment_$sub.txt --ntasks=1 --partition=express --mem-per-cpu=9192 --time=2:00:00 segment_$sub.sh 
 popd
 
 done