====== BET Example Cluster Script ======
The script below will run FSL's BET (brain extraction tool) on any MR image, provided it is in an image format that FSL can read.  

===== qsub_fsl_bet =====
Example usage:
<code>
[user@head ~]$ qsub -v EXPERIMENT=Dummy.01 qsub_fsl_bet EXPERIMENT/Data/Anat/99999/srs500.hdr \
 EXPERIMENT/Data/Anat/99999 anat_brain
</code>

Copy and edit code below:
<code bash>
#!/bin/sh

# This is a BIAC template script for jobs on the cluster
# You have to provide the Experiment on command line  
# when you submit the job the cluster.
#
# >  qsub -v EXPERIMENT=Dummy.01  script.sh args
#
# 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 --
# User script goes here

# Need to input global EXPERIMENT, and inputs INFILE, OUTDIR, and OUTPRE
# INFILE is the file path and name of the file to process
# OUTDIR is where the output folder will go
# OUTPRE is the output prefix of the file
# Example:  qsub -v EXPERIMENT=Dummy.01 qsub_fsl_bet \
# EXPERIMENT/Data/Anat/99999/srs500.hdr \
# EXPERIMENT/Data/Anat/99999 anat_brain

INFILE=$1
OUTDIR=$2
OUTPRE=$3

# In this bash syntax, the preceding string "EXPERIMENT" is removed 
# from the string $INFILE.  
# Example:
# If INFILE = EXPERIMENT/Data/Anat/99999/srs500.hdr
# running ${INFILE#EXPERIMENT}, it becomes:
# /Data/Anat/99999/srs500.hdr

INFILE=${EXPERIMENT}${INFILE#EXPERIMENT}
OUTDIR=${EXPERIMENT}${OUTDIR#EXPERIMENT}
BETVALUE=0.05

mkdir -p $OUTDIR
echo "bet $INFILE $OUTDIR/$OUTPRE -f $BETVALUE"
bet $INFILE $OUTDIR/$OUTPRE -f $BETVALUE


# -- 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-- 

</code>