#!/bin/sh

#   tbss_reg - TBSS nonlinear registration
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2005-2007 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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#   FMRIB Software Library, Release 4.0 (c) 2007, The University of
#   Oxford (the "Software")
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#   
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Usage() {
    echo ""
    echo "Usage: tbss_reg <input_fileroot> <reference_fileroot> [-a] [-A]"
    echo "-a : apply transformation to input (as well as estimating it)"
    echo "-A : affine-only registration"
    echo "tbss_reg MUST be run with both files in current directory and no pathnames specified"
    echo ""
    exit 1
}

D=${FSLDIR}/bin/DR

[ "$2" = "" ] && Usage
INPUT=`${FSLDIR}/bin/remove_ext $1`
REFERENCE=`${FSLDIR}/bin/remove_ext $2`
I2R=${INPUT}_to_${REFERENCE}
shift 2

apply=0
affine=0
while [ _$1 != _ ] ; do
    if [ $1 = -a ] ; then
	apply=1
        shift
    elif [ $1 = -A ] ; then
        affine=1
        shift
    else
        Usage
    fi
done


# do the registration
${D}/areg ${REFERENCE}.hdr ${INPUT}.hdr -dofout ${I2R}_affine.dof -parameter ${D}/affineCC.par

if [ $affine = 1 ] ; then

    if [ $apply = 1 ] ; then
	${D}/transformation ${INPUT}.hdr ${I2R}.hdr -dofin ${I2R}_affine.dof -linear -target ${REFERENCE}.hdr
    fi
    
else

    ${D}/nreg ${REFERENCE}.hdr ${INPUT}.hdr -dofin ${I2R}_affine.dof -dofout ${I2R}_nonlinear.dof -ds 20 -Tp 0 -parameter ${D}/nonlinearCC.par

    if [ $apply = 1 ] ; then
	${D}/transformation ${INPUT}.hdr ${I2R}.hdr -dofin ${I2R}_nonlinear.dof -linear -target ${REFERENCE}.hdr
    fi

    # now estimate the mean deformation
    T=${I2R}_tmp
    mkdir -p $T
    ${D}/dof2gipl ${REFERENCE}.hdr ${INPUT}_to_${REFERENCE}_affine.dof ${T}/grotAx.hdr ${T}/grotAy.hdr ${T}/grotAz.hdr
    ${D}/dof2gipl ${REFERENCE}.hdr ${INPUT}_to_${REFERENCE}_nonlinear.dof ${T}/grotNx.hdr ${T}/grotNy.hdr ${T}/grotNz.hdr
    cd $T
    $FSLDIR/bin/fslmaths grotNx -sub grotAx -sqr grotSx
    $FSLDIR/bin/fslmaths grotNy -sub grotAy -sqr grotSy
    $FSLDIR/bin/fslmaths grotNz -sub grotAz -sqr grotSz
    $FSLDIR/bin/fslmaths grotSx -add grotSy -add grotSz -mas ../$REFERENCE grotSS
    $FSLDIR/bin/fslstats grotSS -M -P 50 > ../${I2R}_nonlinear.msf
    cd ..
    /bin/rm -rf $T

    $FSLDIR/bin/dof2warp $INPUT $REFERENCE ${I2R}_nonlinear.dof ${I2R}_nonlinear
fi

