# To run a local gyrification index (LGI) for several runs in parallel

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#!/bin/bash

#Make a jobs directory in your scratch space to store all the job scripts and results
mkdir /scratch/user/blazerid/jobs

#Define some variables to be used later
jobs=/scratch/user/blazerid/jobs
sub=PATH_TO_SUBJECTS_DIRECTORY

for patient in ls -1 $sub do SUBJECTS_DIR=PATH_TO_SUBJECTS_DIRECTORY echo "#!/bin/bash #$ -S /bin/bash
#$-cwd # #$ -N recon-all-$patient # Set the hard and soft run time limits (ex: 1hour/58 min) #$ -l h_rt=36:00:00,s_rt=30:55:00,vf=3000M
#$-j y #$ -M blazerid@uab.edu
#$-m eas module load matlab/R2012a module load freesurfer/freesurfer-5.3.0 SUBJECTS_DIR=PATH_TO_SUBJECTS_DIRECTORY recon-all -s$patient -localGI" >> $patient.job qsub$patient.job
done


You can copy the above script in your Jobs Directory in the scratch space and put appropriate values in place of blazerid and PATH_TO_SUBJECTS_DIRECTORY

NOTE: For PATH_TO_SUBJECTS_DIRECTORY, give the full path.
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