Commit 1247c8f3 authored by Joe Lyons's avatar Joe Lyons

add clusterReconAll for FS v6

parent ce563d93
#!/bin/bash
# Take all arguments and pass them through to recon-all on the cluster
# We source the FS config file here so that SUBJECTS/FUNCTIONALS_DIR are
# set if the user hasn't already set them
. /etc/freesurfer/6.0/freesurfer.sh
mkdir -p /scratch$HOME/logs
qsub -j y -o /scratch$HOME/logs << EOF
#!/bin/bash
#$ -N FSRECON
. /etc/freesurfer/6.0/freesurfer.sh
set -e
set -u
export SUBJECTS_DIR=${SUBJECTS_DIR}
export FUNCTIONALS_DIR=${FUNCTIONALS_DIR}
recon-all $@
EOF
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