====== runFREE.sh Example Script ======
The example script below will run freesurfer segmentation (using recon-all) on a hi-resolution anatomical series.
**NOTE**: Please be considerate when running freesurfer scripts on the cluster. Since Freesurfer can take over a day to complete, please do not submit too many jobs as other users will have to wait for these processes to complete before theirs will start.
===== submitting runFREE.sh =====
Example usage:
[user@head ~]$ qsub -v EXPERIMENT=Dummy.01 RunFree.sh 20071031_12345 Data/Anat/20071031_12345/series300
#!/bin/sh
# This is a BIAC template script for running FreeSurfer reconstruction on the cluster
# You can use this script with no modification by entering the following command on
# the cluster head-node:
#
# > qsub -v EXPERIMENT=MyExperiment RunFree.sh SubjID SeriesDir
# where:
# MyExperiment is your BIAC experiment name (eg. Expt.02)
# SubjID is the name you want to assign for this subject reconstruction
# (eg. 1234 or subj21)
# SeriesDir is the directory path to get to your anatomical DICOM images for the
# subject you want to reconstruct, within your MyExperiment directory
# (eg. Data/Anat/20110101_12345/series300 )
#
# The job will create an output directory for this subject, within your MyExperiment
# directory at:
# Analysis/freesurfer/SubjID
#
# Note: The QSUB command will automatically insert your email address to notify you of job
# status.
#
# If you want to modify this template script, there are 2 USER sections:
# 1. USER DIRECTIVE: If you want mail notifications when
# your job is completed or fails you need to set the
# correct email address.
#
# 2. USER SCRIPT: Add the user script in this section.
# Within this section you can access your experiment
# folder using $EXPERIMENT. All paths are relative to this variable
# eg: $EXPERIMENT/Data $EXPERIMENT/Analysis
# By default all terminal output is routed to the " Analysis "
# folder under the Experiment directory i.e. $EXPERIMENT/Analysis
# To change this path, set the OUTDIR variable in this section
# to another location under your experiment folder
# eg: OUTDIR=$EXPERIMENT/Analysis/GridOut
# By default on successful completion the job will return 0
# If you need to set another return code, set the RETURNCODE
# variable in this section. To avoid conflict with system return
# codes, set a RETURNCODE higher than 100.
# eg: RETURNCODE=110
# Arguments to the USER SCRIPT are accessible in the usual fashion
# eg: $1 $2 $3
# The remaining sections are setup related and don't require
# modifications for most scripts. They are critical for access
# to your data
# --- BEGIN GLOBAL DIRECTIVE --
#$ -S /bin/sh
#$ -o $HOME/$JOB_NAME.$JOB_ID.out
#$ -e $HOME/$JOB_NAME.$JOB_ID.out
#$ -m ea
# -- END GLOBAL DIRECTIVE --
# -- BEGIN PRE-USER --
#Name of experiment whose data you want to access
EXPERIMENT=${EXPERIMENT:?"Experiment not provided"}
EXPERIMENT=`findexp $EXPERIMENT`
EXPERIMENT=${EXPERIMENT:?"Returned NULL Experiment"}
if [ $EXPERIMENT = "ERROR" ]
then
exit 32
else
#Timestamp
echo "----JOB [$JOB_NAME.$JOB_ID] START [`date`] on HOST [$HOSTNAME]----"
# -- END PRE-USER --
# **********************************************************
# -- BEGIN USER DIRECTIVE --
# Send notifications to the following address
#$ -M user@somewhere.edu
# -- END USER DIRECTIVE --
# -- BEGIN USER SCRIPT --
SUBJ=$1
SERIESDIR=$2
RAWDIR=${EXPERIMENT}/${SERIESDIR}
FREEOUT=${EXPERIMENT}/Analysis/freesurfer
#if out directory doesn't exist, then make it
if [ ! -d "$FREEOUT" ]; then
mkdir -p $FREEOUT
fi
#if the fsaverage subject doesn't exist there, then copy it
for freedirs in fsaverage lh.EC_average rh.EC_average; do
if [ ! -d "${FREEOUT}/${freedirs}" ]; then
cp -R $FREESURFER_HOME/subjects/${freedirs} $FREEOUT/
fi
done
export SUBJECTS_DIR=$FREEOUT
cd $SUBJECTS_DIR
recon-all -i $RAWDIR/*_00001.dcm -s $SUBJ
recon-all -autorecon-all -s $SUBJ
# -- END USER SCRIPT -- #
# **********************************************************
# -- BEGIN POST-USER --
echo "----JOB [$JOB_NAME.$JOB_ID] STOP [`date`]----"
OUTDIR=${OUTDIR:-$EXPERIMENT/Analysis}
mv $HOME/$JOB_NAME.$JOB_ID.out $OUTDIR/$JOB_NAME.$JOB_ID.out
RETURNCODE=${RETURNCODE:-0}
exit $RETURNCODE
fi
# -- END POST USER--