#!/bin/bash
#!/bin/usr/perl
#$ -S /bin/bash
#$ -cwd
#
#$ -N recon-all-emo04
# Set the hard and soft run time limits (ex: 1hour/58 min)
#$ -l h_rt=30:00:00,s_rt=29:55:00
#$ -j y
#$ -M YOUR_EMAIL_ADDRESS
#$ -m eas

# set up FreeSurfer environment variables to export to Cluster Node

FREESURFER_HOME=/usr/local/freesurfer_v5.0.0 ; export FREESURFER_HOME
source /usr/local/freesurfer_v5.0.0/SetUpFreeSurfer.sh
FSFAST_HOME=/usr/local/freesurfer_v5.0.0/fsfast ; export FSTAT_HOME
FSF_OUTPUT_FORMAT=nii ; export FSF_OUTPUT_FORMAT
SUBJECTS_DIR=/home/username/FreeSurfer/FreeSurfer_analysis ; export SUBJECTS_DIR
MNI_DIR=/usr/local/freesurfer/mni ; export MNI_DIR
FSL_DIR=/usr/local/fsl ; export FSL_DIR
PATH=/usr/local/freesurfer_v5.0.0/bin:/usr/local/freesurfer_v5.0.0/fsfast/bin:/usr/local/freesurfer_v5.0.0/mni/bin:/usr/local/fsl/bin:/usr/bin/perl:/usr/local/freesurfer_v5.0.0/bin:/usr/local/freesurfer_v5.0.0/fsfast/bin:/usr/local/fsl/bin:/usr/local/freesurfer_v5.0.0/mni/bin:/usr/sge/bin/lx24-amd64:/usr/sge/bin/lx24-amd64:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/usr/local/bxh-xcede/bin:/usr/local/bxh-xcede/bin/XML:/usr/local/fsl/bin:/usr/local/afni:/usr/local/BrainVoyagerQX:/home/username/bin:/usr/local/bx:/usr/local/caret/bin_linux:/usr/local/bx:/usr/local/caret/bin_linux export PATH

#add freesurfer process you would like to run

sleep 10

recon-all -subjid emo04 -localGI