#!/bin/sh
# --------------PPI FACES TEMPLATE ----------------
#
# This script works with it's partner python, PPI_FACES.sh, and a MATLAB script
# PPI_FACES.m (in Scripts folder on Munin) to run PPI analysis. It
# uses the PPI "button" in SPM to first extract a timeseries from
# based on a user specified roi. It takes in an order number for a group of subjects
# to set the order specific matrices that are used in the PPI analysis. This is
# the "11 regressor model" that should only be used for Faces contrasts other
# than Faces > Shapes. If you want Faces > Shapes please use PPI_ALLFACES.
# If you are interested in CARDS please use PPI_CARDS.
# To minimize user error in entering contrast and order number specific matrices,
# Vanessa decided to hard code the matrices into the .m script, and they are
# set based on the order number variable specified by the user. The script then
# moves into a single subject analysis, and uses the extracted values
# (under PPI.P, PPI.ppi, and PPI.Y) as regressors. Additionally,
# it uses the ART motion outliers from the subject's original BOLD
# preprocessing for the task of interest as an additional regressor.
# Output goes into the user specified folder under Analysis/SPM/Analyzed/(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 --
# ------------------------------------------------------------------------------
# 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
OUTPUTFOL="SUB_OUTPUTFOL_SUB" # This is the user specified name for the output folder under Analyzed/Subject
ORDER="SUB_ORD_SUB" # this is the order number that specifies the matrices to be used:
# [condition#1 1 weight; condition#2 1 weight] etc.
ATASK="SUB_ATASK_SUB" # this is the task that the user is running - since the matrix is specific to the
# task, we can only run 1 at a time
VOIMASKTYPE="SUB_VMASKTYPE_SUB" # the type of VOI mask to make (cube,sphere,mask)
VOINAME="SUB_NAMEOFVOI_SUB" # name that we want our resulting VOI to have
CONTRASTNO=SUB_CONNUM_SUB # this is the number of the contrast from the single subject SPM.mat that we want
# to use to extract values from
SCENTERX=SUB_CENTERSPHEREX_SUB # center voxels of sphere for VOI [x y z]
SCENTERY=SUB_CENTERSPHEREY_SUB
SCENTERZ=SUB_CENTERSPHEREZ_SUB
SRADIUS=SUB_RADIUSSPHERE_SUB # radius of sphere for VOI
BOXDIMX=SUB_DIMBOXX_SUB # Dimensions of the box for the VOI [2 2 2]
BOXDIMY=SUB_DIMBOXY_SUB
BOXDIMZ=SUB_DIMBOXZ_SUB
BOXCENTERX=SUB_CENTERBOXX_SUB # Center of the box for the VOI [-10 -10 -10]
BOXCENTERY=SUB_CENTERBOXY_SUB
BOXCENTERZ=SUB_CENTERBOXZ_SUB
THEVOIMASK="SUB_THEMASKVOI_SUB" # This is the name of a mask to use to make the VOI
# Mask name must include the extension!
VOIMASKTHRESH=SUB_MASKVOITHRESH_SUB # The threshold to use for the VOI mask, should be 1?
CONTRAST="SUB_CONNAME_SUB" # This is the name of the contrast we are interested in (Faces_gr_Shapes)
THRESHDESC="SUB_DESCOFTHRESH_SUB" # This is either "FWE" or "none"
THRESHOLD=SUB_THRESH_SUB # This is the threshold to use to create the individual VOI
EXTENT=SUB_VOXEXT_SUB # The extent threshold (0)
ADJUSTDATA=SUB_DATAADJUST_SUB # Index of the F Contrast
SESSION=SUB_NUMSESS_SUB # Choice of the session number - should be 1?
MASKOTHER="SUB_OTHERMASK_SUB" # If the user wants to mask with another contrast (yes/no)
MASKOTHERCON="SUB_OTHERMASKCON_SUB" # If yes, we need the contrast#, threshold, and inclusive
SUBINCLUDED="SUB_SUBINCLUDED_SUB" # This is the number of subjects folder underROI/PPI/Task (125s)
MASKOTHERTHRESH=SUB_OTHERMASKTHRESH_SUB
MASKOTHERINCLUSIVE="SUB_OTHERMASKINCLUSIVE_SUB"
# Here we check the order number, and exit with error if it isn't 1,2,3, or 4.
if [ $ORDER != "1" ] && [ $ORDER != "2" ] && [ $ORDER != "3" ] && [ $ORDER != "4" ]
then
echo $ORDER " is not a valid order number, exiting."
exit 32;
fi
# Here we make sure the user has specified to run 'faces'.
case $ATASK in
'faces') echo 'Task selected for PPI analysis is faces.'
;;
*) echo "$ATASK is not a valid task name."
echo "...must be faces!";;
esac
#Make the subject's VOI folder and Contrast folder
mkdir -p $EXPERIMENT/Analysis/SPM/Analyzed/$SUBJ/VOIs
mkdir -p $EXPERIMENT/Analysis/SPM/Analyzed/$SUBJ/VOIs/$CONTRAST
#Make the subject specific output directory
mkdir -p $EXPERIMENT/Analysis/SPM/Analyzed/$SUBJ/PPI
mkdir -p $EXPERIMENT/Analysis/SPM/Analyzed/$SUBJ/PPI/$CONTRAST
mkdir -p $EXPERIMENT/Analysis/SPM/Analyzed/$SUBJ/PPI/$CONTRAST/$OUTPUTFOL
# Initialize other variables to pass on to matlab template script
OUTDIR=$EXPERIMENT/Analysis/SPM/Analyzed/$SUBJ/PPI/$CONTRAST/$OUTPUTFOL # This is the output directory
SCRIPTDIR=$EXPERIMENT/Scripts/ # This is the location of our MATLAB script templates
BIACROOT=/usr/local/packages/MATLAB/BIAC # This is where matlab is installed on the custer
# ------------------------------------------------------------------------------
# Step 2: Creation and run of PPI_FACES subject script
# ------------------------------------------------------------------------------
cd $SCRIPTDIR/MATLAB/PPI
# Loop through template script replacing keywords
for i in 'PPI_FACES.m'; do
sed -e 's@SUB_MOUNT_SUB@'$EXPERIMENT'@g' \
-e 's@SUB_OUTPUT_SUB@'$OUTPUTFOL'@g' \
-e 's@SUB_BIACROOT_SUB@'$BIACROOT'@g' \
-e 's@SUB_CONTRASTNO_SUB@'$CONTRASTNO'@g' \
-e 's@SUB_TASK_SUB@'$ATASK'@g' \
-e 's@SUB_ORDER_SUB@'$ORDER'@g' \
-e 's@SUB_VOINAME_SUB@'$VOINAME'@g' \
-e 's@SUB_EXTENT_SUB@'$EXTENT'@g' \
-e 's@SUB_CONTRAST_SUB@'$CONTRAST'@g' \
-e 's@SUB_THETHRESHOLD_SUB@'$THRESHOLD'@g' \
-e 's@SUB_SCRIPTDIR_SUB@'$SCRIPTDIR'@g' \
-e 's@SUB_ADJUSTDATA_SUB@'$ADJUSTDATA'@g' \
-e 's@SUB_SESSION_SUB@'$SESSION'@g' \
-e 's@SUB_THRESHDESC_SUB@'$THRESHDESC'@g' \
-e 's@SUB_MASKOTHER_SUB@'$MASKOTHER'@g' \
-e 's@SUB_MASKOTHERCON_SUB@'$MASKOTHERCON'@g' \
-e 's@SUB_INCLUDEDSUB_SUB@'$SUBINCLUDED'@g' \
-e 's@SUB_MASKOTHERTHRESH_SUB@'$MASKOTHERTHRESH'@g' \
-e 's@SUB_MASKOTHERINCLUSIVE_SUB@'$MASKOTHERINCLUSIVE'@g' \
-e 's@SUB_VOIMASK_SUB@'$THEVOIMASK'@g' \
-e 's@SUB_SPHERERADIUS_SUB@'$SRADIUS'@g' \
-e 's@SUB_SPHERECENTERX_SUB@'$SCENTERX'@g' \
-e 's@SUB_SPHERECENTERY_SUB@'$SCENTERY'@g' \
-e 's@SUB_SPHERECENTERZ_SUB@'$SCENTERZ'@g' \
-e 's@SUB_BOXCENTERX_SUB@'$BOXCENTER'@g' \
-e 's@SUB_BOXCENTERY_SUB@'$BOXCENTER'@g' \
-e 's@SUB_BOXCENTERZ_SUB@'$BOXCENTER'@g' \
-e 's@SUB_VOIMASKTHRESH_SUB@'$VOIMASKTHRESH'@g' \
-e 's@SUB_VOIMASKTYPE_SUB@'$VOIMASKTYPE'@g' \
-e 's@SUB_BOXDIM_SUB@'$BOXDIMX'@g' \
-e 's@SUB_BOXDIM_SUB@'$BOXDIMY'@g' \
-e 's@SUB_BOXDIM_SUB@'$BOXDIMZ'@g' \
-e 's@SUB_SUBJECT_SUB@'$SUBJ'@g' <$i> $OUTDIR/PPI_FACES.m
done
# Change to output directory and run matlab on input script
cd $OUTDIR
# ------------------------------------------------------------------------------
# Step 3: Preparing Virtual Display
# ------------------------------------------------------------------------------
#First we choose an int at random from 100-500, which will be the location in
#memory to allocate the display
RANDINT=$[( $RANDOM % ($[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 < PPI_FACES.m;
echo "Done running PPI_FACES.m in matlab"
# 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${RANDINT};
echo "lock file was deleted";
fi
fi
# -- END USER SCRIPT -- #
# **********************************************************
# -- BEGIN POST-USER --
echo "----JOB [$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--