#!/bin/sh

study=$1
shift

id=$1
shift

tdir=$1
shift

wdir=$1
shift

sok=$1
shift

debug=1

#Now get the uncorrected PETs and register to user space MRI
bsc=`printf "${id}s%04d" $sok`
${FSLDIR}/bin/imcp ${tdir}/${bsc} ${tdir}/${id}_tmp
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${id}_tmp -omat ${tdir}/${bsc}_pet2struc.mat -out ${tdir}/${bsc}_reg
for i in {0..3}; do 
        if [ "$i" != "$sok" ]; then
                tf=`printf "${id}s%04d" $i`
                ${FSLDIR}/bin/imcp ${tdir}/${tf} ${tdir}/${id}_tmp
                ${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${id}_tmp -init ${tdir}/${bsc}_pet2struc.mat -omat ${tdir}/${tf}_pet2struc.mat -out ${tdir}/${tf}_reg
        fi
done
a=`for i in {0..3}; do printf " ${tdir}/${id}s%04d_reg " $i; done`
${FSLDIR}/bin/fslmerge -t ${wdir}/${id}_tmp_mvc $a
${FSLDIR}/bin/mcflirt -in ${wdir}/${id}_tmp_mvc -out ${wdir}/${id}_tmp_corr
${PIPEDIR}/bin/4dmean.pl ${wdir}/${id}_tmp_corr
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${wdir}/${id}_mean -omat ${wdir}/${id}_fbb2struc.mat -out ${wdir}/${id}_fbb

if [ $debug = 0 ] ; then
    rm ${tdir}/${id}_tmp*
    rm ${wdir}/${id}_tmp*
fi