correct_and_average

#!/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=`fslval $1 dim4`;
vols_per_avg=`echo "10k $total_vols $numavgs / p"|dc -`;
fslroi ${1} data 0 ${vols_per_avg};
fslmaths 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
	
	fslroi ${$}${1}_b0_correct ${$}avg_${avg}_scan_${scan} $tmp;
    	scan=`expr $scan + 1`;
    done
    fslmerge -t ${$}avg_${avg}_all `imglob ${$}avg_${avg}_scan_*`
    fslmaths data  -add ${$}avg_${avg}_all data;
    avg=`expr $avg + 1`;
    
done
fslmaths data -div ${numavgs} data;
rm ${$}*