This script is submit once per subject by the python. It performs the main VBM Analysis.
| The script then navigates to DNS/Analysis/Scripts/SPM/VBM, and uses vbm.m as a template script, feeding in all the correct variables and paths. This matlab script is either saved as vbm_1 (for SPM Default) or vbm_2 (for SPGR), and this subject specific copy is saved in the output directory. You can [[http://www.vsoch.com/LONG/Vanessa/MATLAB/SPM/VBM/DNS/vbm8.m | see this script here]] |
#!/bin/sh
# --------------SPM BATCH VBM 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
#
# ----------------------------------------------------
# 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"}
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
# ------------------------------------------------------------------------------
#
# 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
ANATFOLDER=SUB_ANATFOL_SUB # This is the name of the anatomical folder
GMMODULATION=SUB_MODULATIONGM_SUB # This is set to 1, meaning we want the SPM default
ANATNAME=SUB_ANATNAME_SUB
# Set the folder name based on the GMMODULATION choice
if [ $GMMODULATION == 1 ]
then
FOLDER="SPM_Default_Modulation"
fi
if [ $GMMODULATION == 2 ]
then
FOLDER="SPGR"
fi
#Make the subject specific output directories
mkdir -p $EXPERIMENT/Analysis/SPM/Processed/$SUBJ/$ANATFOLDER/$FOLDER
SPGR_OUTDIR=$EXPERIMENT/Analysis/SPM/Processed/$SUBJ/$ANATFOLDER/$FOLDER
# Initialize other variables to pass on to matlab template script
OUTDIR=$EXPERIMENT/Analysis/SPM/Processed/$SUBJ # This is the subject output directory top
SCRIPTDIR=$EXPERIMENT/Scripts/SPM/VBM # This is the location of our MATLAB script templates
BIACROOT=/usr/local/packages/MATLAB/BIAC # This is where matlab is installed on the custer
# Pull the first four characters of the anat name to rename the file:
ANATPRE=$(echo $ANATNAME | cut -c1-6)
# Since we have differing formats, make sure to convert to lowercase.
ANATPRE=$(echo $ANATPRE | tr '[:upper:]' '[:lower:]')
# ------------------------------------------------------------------------------
# Running VBM
# ------------------------------------------------------------------------------
# Change into directory where template exists, save subject specific script
cd $SCRIPTDIR
# Loop through template script replacing keywords
for i in 'vbm8.m'; do
sed -e 's@SUB_BIACROOT_SUB@'$BIACROOT'@g'
-e 's@SUB_SCRIPTDIR_SUB@'$SCRIPTDIR'@g'
-e 's@SUB_SUBJECT_SUB@'$SUBJ'@g'
-e 's@SUB_MOUNT_SUB@'$EXPERIMENT'@g'
-e 's@SUB_NAMEOFANAT_SUB@'$ANATNAME'@g'
-e 's@SUB_GMMODULATION_SUB@'$GMMODULATION'@g'
-e 's@SUB_ANATFOLDER_SUB@'$ANATFOLDER'@g' <$i> $OUTDIR/vbm8_${GMMODULATION}.m
done
# Change to output directory and run matlab on input script
cd $OUTDIR
/usr/local/bin/matlab -nodisplay < vbm8_${GMMODULATION}.m
echo "Done running spm_vbm.m in matlabn"
case $GMMODULATION in
1 )
# Copy data into mprage folder
cd $EXPERIMENT/Analysis/SPM/Processed/$SUBJ/$ANATFOLDER/
cp sm0wp2$ANATNAME.nii $SPGR_OUTDIR/sm0wp2_$ANATPRE.nii
cp wm$ANATNAME.nii $SPGR_OUTDIR/wm_$ANATPRE.nii
cp m0wp2$ANATNAME.nii $SPGR_OUTDIR/m0wp2_$ANATPRE.nii
cp mwp1$ANATNAME.nii $SPGR_OUTDIR/mwp1_$ANATPRE.nii
cp smwp1$ANATNAME.nii $SPGR_OUTDIR/smwp1_$ANATPRE.nii
cp $ANATNAME"_seg8".mat $SPGR_OUTDIR/$ANATPRE"_seg8".mat
cp p$ANATNAME"_seg8".txt $SPGR_OUTDIR/p_$ANATPRE"_seg8".txt
# Delete old files
rm sm0wp2$ANATNAME.nii
rm wm$ANATNAME.nii
rm m0wp2$ANATNAME.nii
rm mwp1$ANATNAME.nii
rm smwp1$ANATNAME.nii
rm $ANATNAME"_seg8".mat
rm p$ANATNAME"_seg8".txt;;
2 )
cd $EXPERIMENT/Analysis/SPM/Processed/$SUBJ/$ANATFOLDER/
cp sm0wp2$ANATNAME.nii $SPGR_OUTDIR/sm0wp2_$ANATPRE.nii
cp sm0wp1$ANATNAME.nii $SPGR_OUTDIR/sm0wp1_$ANATPRE.nii
cp wm$ANATNAME.nii $SPGR_OUTDIR/wm_$ANATPRE.nii
cp m0wp2$ANATNAME.nii $SPGR_OUTDIR/m0wp2_$ANATPRE.nii
cp m0wp1$ANATNAME.nii $SPGR_OUTDIR/m0wp1_$ANATPRE.nii
cp $ANATNAME"_seg8".mat $SPGR_OUTDIR/$ANATPRE"_seg8".mat
cp p$ANATNAME"_seg8".txt $SPGR_OUTDIR/$ANATPRE"_seg8".txt
# Delete old files
rm sm0wp2$ANATNAME.nii
rm sm0wp1$ANATNAME.nii
rm m0wp2$ANATNAME.nii
rm m0wp1$ANATNAME.nii
rm $ANATNAME"_seg8".mat
rm p$ANATNAME"_seg8".txt
rm wm$ANATNAME.nii;;
esac
# -- END USER SCRIPT -- #
# **********************************************************
# -- BEGIN POST-USER --
echo "----JOB [$JOB_NAME.$JOB_ID] STOP [`date`]----"
OUTDIR=${OUTDIR:-$EXPERIMENT/Analysis/SPM/Processed/$SUBJ}
mv $HOME/$JOB_NAME.$JOB_ID.out $OUTDIR/$JOB_NAME.$JOB_ID.out
RETURNCODE=${RETURNCODE:-0}
exit $RETURNCODE
fi
# -- END POST USER--