#!/bin/sh
#-------------BET---------------------------------------
# This script is intended to run a brain extraction on the
# anatomical data, assumed to be in folder 3. It outputs a file
# called anat_brain.nii in the RawData/SUBJECT/3/BET folder
# and takes an input *.nii from the same folder
# ---------WHEN DO I RUN THIS?------------
# In the pipeline, you should first run the data through QA to eliminate any bad apples,
# then convert functional and anatomicals to nifti, and then BET with McFlirt before FEAT
#
# --------WHAT DO I NEED TO CHANGE?------------
# the email to direct the successful run of the script
# check if you want a different OUTDIR path (if not in folder 3, etc)
# the BET value
#------------SUBMISSION ON COMMAND LINE---------------
# [abc1@head ~]$ qsub -v EXPERIMENT=Dummy.01 BET.sh Data/RawData/ *.nii anat_brain 4 111111111
# datadirectory input nifti output file anatfolder SUBJECT ID
# --- 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"}
source /etc/biac_sge.sh
EXPERIMENT=`biacmount $EXPERIMENT`
EXPERIMENT=${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@email.com
# -- END USER DIRECTIVE --
# -- BEGIN USER SCRIPT --
# User script goes here
# Need to input global EXPERIMENT, and inputs DATADIR, INFILE, OUTDIR, ANATFOLD, SUBJECT, and OUTPRE
# DATADIR is the main data directory under EXPERIMENT
# INFILE is the .nii file of the anatomicals to be extracted (*.nii)
# OUTDIR is where the output anat_brain.nii will go - we set it to "BET" in folder 3
# OUTPRE is the output prefix of the file - it should be anat_brain
# SUBJECT is the name of the subject's folder
# ANATFOLD is the name of the anatomicals folder (3)
# Example: qsub -v EXPERIMENT=Dummy.01 BET.sh
# Data/RawData anat.nii anat_brain 345234
DATADIR=$1
INFILE=$2
OUTPRE=$3
ANATFOLD=$4
SUBJECT=$5
# First, we set the output directory to a folder called "BET" in the anatomical folder.
# which we go to and make
OUTDIR=$EXPERIMENT/$DATADIR/$SUBJECT/$ANATFOLD/
cd $OUTDIR
mkdir -p BET
# Then we remove the preceding string "EXPERIMENT" from the string $OUTDIR and $DATADIR
# Example:
# If DATADIR = EXPERIMENT/Data/Anat/99999/srs500.hdr
# running ${INFILE#EXPERIMENT}, it becomes:
# /Data/Anat/99999/srs500.hdr
# DATADIR=${EXPERIMENT}${DATADIR#EXPERIMENT}
# OUTDIR=${EXPERIMENT}${OUTDIR#EXPERIMENT}
# Then we set the BETVALUE, or the threshold that determines how much we remove
# (If you aren't sure, play with this value in the GUI until it looks right!)
BETVALUE=0.225
# Then we print the command, in case we need to check it in the output
echo "bet $INFILE BET/$OUTPRE -f $BETVALUE"
bet $INFILE BET/$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--