#!/bin/sh

study=$1
shift

id=$1
shift

tdir=$1
shift

wdir=$1
shift

#sok=$1
#shift

treshold=$1
shift

debug=1

#Now get the uncorrected PETs and register to user space MRI
bsc=`printf "${id}s%04d" $sok`
${FSLDIR}/bin/fslreorient2std ${tdir}/${bsc} ${tdir}/${bsc}_tmp
if [ $treshold = 0 ] ; then
        ${FSLDIR}/bin/fslmaths ${tdir}/${bsc}_tmp -thr ${treshold} -bin ${tdir}/${bsc}_tmp_fbb_mask
else
        ${FSLDIR}/bin/fslmaths ${tdir}/${bsc}_tmp -thrP ${treshold} -bin ${tdir}/${bsc}_tmp_fbb_mask
fi
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${bsc}_tmp_fbb_mask -omat ${tdir}/${bsc}_tmp_fbb -dof 9
${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${bsc} -applyxfm -init ${tdir}/${bsc}_tmp_fbb -out ${tdir}/${bsc}_reg -omat ${tdir}/${bsc}_pet2struc.mat

for i in {0..3}; do 
        if [ "$i" != "$sok" ]; then
                tf=`printf "${id}s%04d" $i`
                ${FSLDIR}/bin/fslreorient2std ${tdir}/${tf} ${tdir}/${id}_tmp
                if [ $treshold = 0 ] ; then
                        ${FSLDIR}/bin/fslmaths ${tdir}/${id}_tmp -thr ${treshold} -bin ${tdir}/${tf}_tmp_fbb_mask
                else
                        ${FSLDIR}/bin/fslmaths ${tdir}/${id}_tmp -thrP ${treshold} -bin ${tdir}/${tf}_tmp_fbb_mask
                fi
                ${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${tf}_tmp_fbb_mask -omat ${tdir}/${tf}_tmp_fbb -init ${tdir}/${bsc}_pet2struc.mat -dof 9
                ${FSLDIR}/bin/flirt -ref ${wdir}/${id}_struc -in ${tdir}/${tf} -applyxfm -init ${tdir}/${tf}_tmp_fbb -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