#!/bin/sh
#This file is run following second level analyses to complete a ROI analysis.
#1. Extracts contrast values (runs featquery on a selected set of COPE images for a selected set of FEAT outputs).
#2. Summarizes these into a txt/xls document (currently takes 24 single subject directories).
#Chris Benjamin 08-20-2011
COPENUMS=”cope1 cope2″
#path name for the folder containing the ROI you’d like to interrogate
ROIPATH=’/path/ROI_rfx/’
#the roi themseleves. Name of both the roi, and the output forlder. Do not include .nii.gz
FQ_OUTPUTDIRNAMES=”roi_dir_name1
roi_dir_name2″
#the image format
IMAGEFORMAT=’.nii.gz’
#name of the folder you want all output folders spat into.
FOLDERFORDATA=’foi_output_fqengine’
echo ‘Starting featquery.’
#featquery script, batched.
for FQ_OUTPUTDIRNAME in $FQ_OUTPUTDIRNAMES ; do
echo ${FQ_OUTPUTDIRNAME}
date -u
for COPENUM in $COPENUMS ; do
echo ${COPENUM}
/usr/share/fsl/4.1/bin/featquery nparticipants PATH_TO_GFEAT_FOLDER_FOR_ALL_nparticipants 1 stats/cope1 ${FQ_OUTPUTDIRNAME} -p -s $ROIPATH${FQ_OUTPUTDIRNAME}$IMAGEFORMAT
done
done
echo ‘… featqueries finished. Summarizing data …’
#Now summarize all the actual cope values into text files.
#make a folder for the cope values to be spat out into, and move into it.
mkdir $FOLDERFORDATA
cd $FOLDERFORDATA
#For each featqueried output
for FQ_OUTPUTDIRNAME in $FQ_OUTPUTDIRNAMES ; do
echo ${FQ_OUTPUTDIRNAME}
date -u
#create a summary file to hold all of the output from this featquery (region of interest)
SUMMARYFILE=”roi_summary_${FQ_OUTPUTDIRNAME}.xls”
touch ${SUMMARYFILE}
#For each cope…
for COPENUM in $COPENUMS ; do
echo $COPENUM
#Print cope number into summary file
echo $COPENUM ‘\t\n’ >> ${SUMMARYFILE}
#Input directories.
#controls
INPUTDIRS=”PATH_TO_GFEAT_FOLDER_FOR_ALL_nparticipants_group1
E.G. /path/PT_ID/task_folder.gfeat/${COPENUM}.feat”
#musicians
INPUTDIRS2=”PATH_TO_GFEAT_FOLDER_FOR_ALL_nparticipants_group2
E.G. /path/PT_ID/task_folder.gfeat/${COPENUM}.feat”
#CREATE SEPARATE OUTPUT FILE FOR WRITING DOCS TO
OUTPUTFILE=”${COPENUM}${FQ_OUTPUTDIRNAME}.txt”
#COMPILE ALL OF THE COPE VALUES.
touch ${OUTPUTFILE}
for INPUTDIR in $INPUTDIRS ; do
#print file location
echo $INPUTDIR ‘\t’ >> ${OUTPUTFILE}
#print cope mean
awk ‘NF{printf(“\t%f\n”, $6)}’ ${INPUTDIR}/$FQ_OUTPUTDIRNAME/report.txt >> ${OUTPUTFILE}
#print file location
echo $INPUTDIR ‘\t’ >> ${SUMMARYFILE}
#print cope mean
awk ‘NF{printf(“\t%f\n”, $6)}’ ${INPUTDIR}/$FQ_OUTPUTDIRNAME/report.txt >> ${SUMMARYFILE}
done
echo “\nGroup 2\n” >> ${OUTPUTFILE}
for INPUTDIR2 in $INPUTDIRS2 ; do
#print file location
echo $INPUTDIR2 ‘\t’ >> ${OUTPUTFILE}
#print cope mean
awk ‘NF{printf(“\t%f\n”, $6)}’ ${INPUTDIR2}/$FQ_OUTPUTDIRNAME/report.txt >> ${OUTPUTFILE}
#print file location
echo $INPUTDIR2 ‘\t’ >> ${SUMMARYFILE}
#print cope mean
awk ‘NF{printf(“\t%f\n”, $6)}’ ${INPUTDIR2}/$FQ_OUTPUTDIRNAME/report.txt >> ${SUMMARYFILE}
done
echo ‘\n\n’ >> ${SUMMARYFILE}
done
done
echo ‘finished.’
date -u
npsy 