#!/bin/sh
# ---------------VOX_MATRIX TEMPLATE ----------------
#
# This script takes preprocessed SPM images and creates
# a matrix of all voxel values within a certain mask
# and threshold specified by the user. Input comes from
# Data/SPM(version)/AllProcessedData/(Subject) and output
# goes to Analysis/Matrices/(Design)/(Subject)
#
# ----------------------------------------------------
# --- 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 --
# -- BEGIN USER SCRIPT --
# User script goes here
# ------------------------------------------------------------------------------
# Step 1: 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
SPMVER=SUB_SPMVER_SUB # This is the version of SPM for swuf images
TASK=SUB_TASKNAME_SUB # This is the name of the task folder underAllProcessedData
IMG_PRE=SUB_IMGPRE_SUB # The image prefix (swrf for SPM2, swu for other versions)
OUTPUTFOL=SUB_OUTPUTFOL_SUB # This is the name of the output folder under Matrices/...
NUMIMAGES=SUB_NUM_IMAGES_SUB # This is the number of images in the functional task
# MASK 1
MASKTYPE=SUB_MTYPE_SUB # This is the mask category folder under ROI/Masks
MASKFILE=SUB_MASKFILE_SUB # This is the full name of the mask image
THRESH=SUB_THRESHOLD_SUB # This is the masking threshold
# MASK 2
MASKTWO=SUB_YESTWOMASK_SUB
MASKTWOTYPE=SUB_MTWOTYPE_SUB
MASKTWOFILE=SUB_MASKTWOFILE_SUB
THRESHTWO=SUB_THRESHOLDTWO_SUB
#Navigate to the subject's folder with the preprocessed swu/swrf images:
cd $EXPERIMENT/Data/$SPMVER/AllProcessedData/$SUBJ/$TASK
#Make a directory to hold the swrf images for processing in the script, and subject outdir
mkdir -p $EXPERIMENT/Data/$SPMVER/AllProcessedData/$SUBJ/$TASK/renamed
mkdir -p $EXPERIMENT/Analysis/Matrices/$TASK/$OUTPUTFOL/$SUBJ
#Set directories
SCRIPTDIR=$EXPERIMENT/Scripts/MATLAB
OUTDIR=$EXPERIMENT/Analysis/Matrices/$TASK/$OUTPUTFOL/$SUBJ
BIACROOT=/usr/local/packages/MATLAB/BIAC
# ------------------------------------------------------------------------------
# Step 2: Image Preparation
# ------------------------------------------------------------------------------
# Copy all swu/swrf .img images into the new renamed directory
countVar=1;
for file in $IMG_PRE*.img
do
if (($countVar < 10)); then
cp $file $EXPERIMENT/Data/$SPMVER/AllProcessedData/$SUBJ/$TASK/renamed/V000$countVar.img
fi
if (($countVar < 100)); then
if (($countVar >= 10)); then
cp $file $EXPERIMENT/Data/$SPMVER/AllProcessedData/$SUBJ/$TASK/renamed/V00$countVar.img
fi
fi
if (($countVar >= 100)); then
cp $file $EXPERIMENT/Data/$SPMVER/AllProcessedData/$SUBJ/$TASK/renamed/V0$countVar.img
fi
let "countVar += 1";
done
#Copy all .hdr images into the new renamed directory
countVar=1;
for file in $IMG_PRE*.hdr
do
if (($countVar < 10)); then
cp $file $EXPERIMENT/Data/$SPMVER/AllProcessedData/$SUBJ/$TASK/renamed/V000$countVar.hdr
fi
if (($countVar < 100)); then
if (($countVar >= 10)); then
cp $file $EXPERIMENT/Data/$SPMVER/AllProcessedData/$SUBJ/$TASK/renamed/V00$countVar.hdr
fi
fi
if (($countVar >= 100)); then
cp $file $EXPERIMENT/Data/$SPMVER/AllProcessedData/$SUBJ/$TASK/renamed/V0$countVar.hdr
fi
let "countVar += 1";
done
# ------------------------------------------------------------------------------
# Step 3: Matrix Creation
# ------------------------------------------------------------------------------
# Change into directory where template exists, save subject specific script
cd $SCRIPTDIR
# Loop through template script replacing keywords
for i in 'vox_extract_cluster.m'; do
sed -e 's@SUB_BIACROOT_SUB@'$BIACROOT'@g' \
-e 's@SUB_SCRIPTDIR_SUB@'$SCRIPTDIR'@g' \
-e 's@SUB_SUBJECT_SUB@'$SUBJ'@g' \
-e 's@SUB_MOUNT_SUB@'$EXPERIMENT'@g' \
-e 's@SUB_SPM_SUB@'$SPMVER'@g' \
-e 's@SUB_TASK_SUB@'$TASK'@g' \
-e 's@SUB_MASKTYPE_SUB@'$MASKTYPE'@g' \
-e 's@SUB_MASKTWOTYPE_SUB@'$MASKTWOTYPE'@g' \
-e 's@SUB_MASKTWONAME_SUB@'$MASKTWOFILE'@g' \
-e 's@SUB_MASKTWO_SUB@'$MASKTWO'@g' \
-e 's@SUB_MINTHRESHTWO_SUB@'$THRESHTWO'@g' \
-e 's@SUB_BIACROOT_SUB@'$BIACROOT'@g' \
-e 's@SUB_MINTHRESH_SUB@'$THRESH'@g' \
-e 's@SUB_NUMIMAGES_SUB@'$NUMIMAGES'@g' \
-e 's@SUB_MASKNAME_SUB@'$MASKFILE'@g' <$i> $OUTDIR/vox_extract_${RUN}.m
done
# Change to output directory and run matlab on input script
cd $OUTDIR
/usr/local/matlab2009b/bin/matlab -nodisplay < vox_extract_${RUN}.m
echo "Done running vox_matrix.m in matlab"
# ------------------------------------------------------------------------------
# Step 4: File Cleanup and Matrix Copy
# ------------------------------------------------------------------------------
#Return to the subject specific folder to delete the renamed files and copy the matrix
cd $EXPERIMENT/Data/$SPMVER/AllProcessedData/$SUBJ/$TASK/renamed
cp voxvalues.mat $OUTDIR/$SUBJ'_gm'.mat
rm V*
rm voxvalues.mat
cd $EXPERIMENT/Data/$SPMVER/AllProcessedData/$SUBJ/$TASK
rmdir renamed
cd $OUTDIR
rm vox_extract_${RUN}.m
# -- END USER SCRIPT -- #
# **********************************************************
# -- BEGIN POST-USER --
echo "----JOB [$JOB_NAME.$JOB_ID] STOP [`date`]----"
OUTDIR=${OUTDIR:-$EXPERIMENT/Analysis/Matrices/$TASK/$OUTPUTFOL/$SUBJ}
mv $HOME/$JOB_NAME.$JOB_ID.out $OUTDIR/$JOB_NAME.$JOB_ID.out
RETURNCODE=${RETURNCODE:-0}
exit $RETURNCODE
fi
# -- END POST USER--