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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 $USER_SCRATCH/jobs

#Define some variables to be used later
jobs=$USER_SCRATCH/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 YOUR_EMAIL_ADDRESS
#$ -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 value in place of YOUR_EMAIL_ADDRESS and PATH_TO_SUBJECTS_DIRECTORY

NOTE: For PATH_TO_SUBJECTS_DIRECTORY, give the full path.