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.