#!/bin/sh

#   pairreg - perform registration of pairs keeping skull scaling const
#
#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
#
#   Copyright (C) 1999-2004 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
#   http://www.fmrib.ox.ac.uk/fsl
#   fsl@fmrib.ox.ac.uk
#   
#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
#   Imaging of the Brain), Department of Clinical Neurology, Oxford
#   University, Oxford, UK
#   
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if [ $# -lt 5 ] ; then
 echo "Usage: $0 brain1 brain2 skull1 skull2 outputmatrix [extra flirt args]"
 echo
 echo "  NB: brain1 and skull1 are used as -ref arguments internally"
 exit 1
fi

bref=$1; export bref
bin=$2; export bin
sref=$3; export sref
sin=$4; export sin
matf=$5; export matf
shift 5
args=$* ; export args

flirt=${FSLDIR}/bin/flirt ; export flirt

$flirt -in $bin -ref $bref -schedule ${FSLDIR}/etc/flirtsch/pairreg1.sch -omat $matf.1.$$ $args
$flirt -in $sin -ref $sref -init $matf.1.$$ -schedule ${FSLDIR}/etc/flirtsch/pairreg2.sch -omat $matf.2.$$ $args
${FSLDIR}/bin/convert_xfm -fixscaleskew $matf.2.$$ $matf.1.$$ -omat $matf.3.$$
$flirt -in $bin -ref $bref -init $matf.3.$$ -schedule ${FSLDIR}/etc/flirtsch/pairreg3.sch -omat $matf $args
# tidy up the temporary matrices
rm -f $matf.1.$$ $matf.2.$$ $matf.3.$$