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#!/bin/sh
# Copyright (C) 2004 University of Oxford
#
# SHCOPYRIGHT
usage()
{
echo "Usage : $0 <big4D dataset> <avg file>"
echo ""
echo " This script assumes that there are 3"
echo " separate averages of 0, 29, 0, 31, 0, 0, 0 b-values"
echo " You need to also run Make_bvecs in matlab"
echo " <artefactfile> is optional"
exit 1
}
[ $# -lt 2 ] && usage
data=`remove_ext ${1}`;
if [ `imtest $data` -eq 0 ];then
echo "Cannot find image called $1";
exit
fi
avgfile=$2;
if [ ! -e $avgfile ];then
echo " Cannot find $2"
exit
fi
numlines=`cat $avgfile |grep -v '^ *$'|wc -l`;
numavgs=`expr $numlines - 1`;
scans_per_avg=`cat $avgfile |sed 's/, *$/ /g'|sed 's/[^,]/ /g'|sed -n '1p'|wc -w`;
scans_per_avg=`expr $scans_per_avg + 1`
b0_numbers=`cat $avgfile |grep -v '^ *$' |sed -n "${numlines}p"`;
ab0=`echo $b0_numbers |awk '{print \$1}'`
eddy_correct ${1} ${$}${1}_b0_correct $ab0
total_vols=`avwval $1 dim4`;
vols_per_avg=`echo "10k $total_vols $numavgs / p"|dc -`;
avwroi ${1} data 0 ${vols_per_avg};
avwmaths data -mul 0 data;
avg=1;scan=1;
while [ ${avg} -le ${numavgs} ]; do
scan=1
#echo ${scan} ${scans_per_avg}
while [ ${scan} -le ${scans_per_avg} ]; do
tmp=`cat $avgfile |sed -n "${avg}p"|awk -F , "{ print \\$$scan }"`;
echo $avg $scan $tmp $vols_per_avg
avwroi ${$}${1}_b0_correct ${$}avg_${avg}_scan_${scan} $tmp;
scan=`expr $scan + 1`;
done
avwmerge -t ${$}avg_${avg}_all `imglob -oneperimage ${$}avg_${avg}_scan_*`
avwmaths data -add ${$}avg_${avg}_all data;
avg=`expr $avg + 1`;
done
avwmaths data -div ${numavgs} data;
rm ${$}*