#!/bin/sh
# --------------SPM BATCH DTI TEMPLATE ----------------
#
# This script takes anatomical and functional data located under
# Data/fund and Data/anat and performs all preprocessing
# by creating and utilizing two matlab scripts, and running spm
# After this script is run, output should be visually checked
#
# ----------------------------------------------------
# --- 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 SUB_USEREMAIL_SUB
# -- END USER DIRECTIVE --
# ------------------------------------------------------------------------------
# Variables and Path Preparation
# ------------------------------------------------------------------------------
# Initialize input variables (fed in via python script)
SUBJ=SUB_SUBNUM_SUB # This is the full subject folder name under Data
RUN=SUB_RUNNUM_SUB # This is a run number, if applicable
TWODATASETS=SUB_TWODATASETS_SUB # yes indicates that the group of subjects has 2 DTI runs
#Make the subject specific output directories
mkdir -p $EXPERIMENT/Analysis/DTI/SPM/$SUBJ
mkdir -p $EXPERIMENT/Analysis/DTI/SPM/$SUBJ/FA
mkdir -p $EXPERIMENT/Analysis/DTI/SPM/$SUBJ/raw #here we put the raw DTI images
DTIFOLDER1=SUB_DTIFOLDER1_SUB # This is the name of the first DTI folder (series008)
DTIFOLDER2=SUB_DTIFOLDER2_SUB # This is the name of the second DTI folder (series009)
# We need the abbreviated numbers below to feed into the image names
SUBPRE=$(echo $SUBJ | cut -c1-5) # This is just the exam number, extracted from the full name
FOLDER1PRE=$(echo $DTIFOLDER1 | cut -c7-9)
FOLDER2PRE=$(echo $DTIFOLDER2 | cut -c7-9)
# Initialize other variables to pass on to matlab template script
OUTDIR=$EXPERIMENT/Analysis/DTI/SPM/$SUBJ # This is the location of the subject's output directory
FAOUTPUT=$EXPERIMENT/Analysis/DTI/SPM/$SUBJ/FA # This is the location of the FA output folder
FOLDERPATH1=$EXPERIMENT/Data/Anat/$DTIFOLDER1 # This is the full path of DTI folder 1
FOLDERPATH2=$EXPERIMENT/Data/Anat/$DTIFOLDER2 # This is the full path of DTI folder 2
# Cluster / BIAC variables
SCRIPTDIR=$EXPERIMENT/Scripts/SPM # This is the location of our MATLAB script templates
BIACROOT=/usr/local/packages/MATLAB/BIAC # This is where matlab is installed on the cluster
# ------------------------------------------------------------------------------
# Step 1: Image Renaming and Moving
# ------------------------------------------------------------------------------
##########################################################################
# DTI Folder One
##########################################################################
cd $EXPERIMENT/Data/Anat/$SUBJ
# Go to the subject DTI data directory to rename and move images
cd $DTIFOLDER1
#Prepare the DTI images
for file in bia5*.*
do
cp $file $EXPERIMENT/Analysis/DTI/SPM/$SUBJ/raw/
done
##########################################################################
# DTI Folder Two
##########################################################################
if [ $TWODATASETS == 'yes' ]; then
cd $EXPERIMENT/Data/Anat/$SUBJ/$DTIFOLDER2
for file in bia5*.*
do
cp $file $EXPERIMENT/Analysis/DTI/SPM/$SUBJ/raw/
done
fi
# ------------------------------------------------------------------------------
# Step 2: Dicom Conversion to Output Folders
# ------------------------------------------------------------------------------
# Change into directory where template exists, save subject specific script
cd $SCRIPTDIR
# Loop through template script replacing keywords
for i in 'spm_DTI2_1.m'; do
sed -e 's@SUB_BIACROOT_SUB@'$BIACROOT'@g' \
-e 's@SUB_SCRIPTDIR_SUB@'$SCRIPTDIR'@g' \
-e 's@SUB_FOLDER1PRE_SUB@'$FOLDER1PRE'@g' \
-e 's@SUB_FOLDER2PRE_SUB@'$FOLDER2PRE'@g' \
-e 's@SUB_SUBJECT_SUB@'$SUBJ'@g' \
-e 's@SUB_SUBPRE_SUB@'$SUBPRE'@g' \
-e 's@SUB_TWORUNS_SUB@'$TWODATASETS'@g' \
-e 's@SUB_MOUNT_SUB@'$EXPERIMENT'@g' <$i> $OUTDIR/spm_DTI2_1_${RUN}.m
done
# Change to output directory and run matlab on input script
cd $OUTDIR
/usr/local/bin/matlab -nodisplay < spm_DTI2_1_${RUN}.m
echo "Done running spm_DTI2_1.m in matlab"
# ------------------------------------------------------------------------------
# Step 3: DTI Single Subject Processing
# ------------------------------------------------------------------------------
# Change into directory where template exists, save subject specific script
cd $SCRIPTDIR
# Loop through template script replacing keywords
for i in 'spm_DTI2_2.m'; do
sed -e 's@SUB_MOUNT_SUB@'$EXPERIMENT'@g' \
-e 's@SUB_BIACROOT_SUB@'$BIACROOT'@g' \
-e 's@SUB_FOLDER1PRE_SUB@'$FOLDER1PRE'@g' \
-e 's@SUB_FOLDER2PRE_SUB@'$FOLDER2PRE'@g' \
-e 's@SUB_SCRIPTDIR_SUB@'$SCRIPTDIR'@g' \
-e 's@SUB_TWORUNS_SUB@'$TWODATASETS'@g' \
-e 's@SUB_SUBJECT_SUB@'$SUBJ'@g' <$i> $OUTDIR/spm_DTI2_2_${RUN}.m
done
# Change to output directory and run matlab on input script
cd $OUTDIR
echo "Changed to output directory";
# ------------------------------------------------------------------------------
# Step 4. Preparing Virtual Display
# ------------------------------------------------------------------------------
#First we choose an int at random from 100-500, which will be the location in
#memory to allocate the display
RANDINT=$[( $RANDOM % ($[500 - 100] + 1)) + 100 ]
echo "the random integer for Xvfb is ${RANDINT}";
#Now we need to see if this number is already being used for Xvfb on the node. We can
#tell because when it is active, it will have a "lock file"
while [ -e "/tmp/.X11-unix/X${RANDINT}" ]
do
echo "lock file was already created for $RANDINT";
echo "Trying a new number...";
RANDINT=$[( $RANDOM % ($[500 - 100] + 1)) + 100 ]
echo "the random integer for Xvfb is ${RANDINT}";
done
#Initialize Xvfb, put buffer output in TEMP directory
Xvfb :$RANDINT -fbdir $TMPDIR &
/usr/local/bin/matlab -display :$RANDINT < spm_DTI2_2_${RUN}.m
echo "Done running spm_DTI_2.m in matlab";
# ------------------------------------------------------------------------------
# Step 5. Cleanup!
# ------------------------------------------------------------------------------
#If the lock was created, delete it
if [ -e "/tmp/.X11-unix/X${RANDINT}" ]
then
echo "lock file was created";
echo "cleaning up my lock file";
rm /tmp/.X${RANDINT}-lock;
rm /tmp/.X11-unix/X${RANDINT};
echo "lock file was deleted";
fi
# once script is working perfectly, enable these to get rid of raw files
cd $OUTDIR/raw
rm *.dcm
# -- END USER SCRIPT -- #
# **********************************************************
# -- BEGIN POST-USER --
echo "----JOB [$JOB_NAME.$JOB_ID] STOP [`date`]----"
OUTDIR=${OUTDIR:-$EXPERIMENT/Analysis/DTI/SPM/$SUBJ}
mv $HOME/$JOB_NAME.$JOB_ID.out $OUTDIR/$JOB_NAME.$JOB_ID.out
RETURNCODE=${RETURNCODE:-0}
exit $RETURNCODE
fi
# -- END POST USER--