#!/bin/sh

#   fslvbm_2_template - FSLVBM template creation
#
#   Gwenaelle Douaud & Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 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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Usage() {
    echo ""
    echo "Usage: fslvbm_2_template [options]"
    echo ""
    echo "-a  : affine registration (recommended)"
    echo "-n  : nonlinear registration"
    echo ""
    exit 1
}

[ "$1" = "" ] && Usage

echo [`date`] [`hostname`] [`uname -a`] [`pwd`] [$0 $@] >> .fslvbmlog

HOWLONG=200
if [ $1 = -a ] ; then
    REG="-A"
    HOWLONG=30
fi

cd FAi

D=${FSLDIR}/bin/DR
export FSLOUTPUTTYPE=ANALYZE

$FSLDIR/bin/fslmaths ${FSLDIR}/data/standard/tissuepriors/avg152T1_gray T
$FSLDIR/bin/fslhd -x T | sed "s/sform_code .*/sform_code = \'0\'/g" > grot.xml
$FSLDIR/bin/fslcreatehd grot.xml T.hdr
/bin/rm grot.xml

### segmentation
/bin/rm -f fslvbm2a
for g in `$FSLDIR/bin/remove_ext *FAi.hdr` ; do
    echo $g
    ### Brain segmentation
    echo -n "$FSLDIR/bin/fast -e -ov ${g}_brain ; " >> fslvbm2a
    ### Transformation of the GM PVE in 16SI datatype and range 0:1000
    echo -n "$FSLDIR/bin/fslmaths ${g}_brain_pve_1 -mul 1000 ${g}_GM -odt short ; " >> fslvbm2a
    ### Creation of the mirror image of each GM
    echo "$FSLDIR/bin/fslswapdim ${g}_GM -x y z ${g}_GM_xflipped" >> fslvbm2a
done
chmod a+x fslvbm2a
fslvbm2a_id=`$FSLDIR/bin/fsl_sub -T 30 -N fslvbm2a -t ./fslvbm2a`
echo Running segmentation: ID=$fslvbm2a_id

### Estimation of the registration parameters of GM and flipped_GM to grey matter standard template
/bin/rm -f fslvbm2b
for g in *FAi.hdr ; do
  g=`$FSLDIR/bin/remove_ext $g`
  echo "${FSLDIR}/bin/tbss_reg ${g}_GM T -a $REG" >> fslvbm2b
  echo "${FSLDIR}/bin/tbss_reg ${g}_GM_xflipped T -a $REG" >> fslvbm2b
done
chmod a+x fslvbm2b
fslvbm2b_id=`$FSLDIR/bin/fsl_sub -j $fslvbm2a_id -T $HOWLONG -N fslvbm2b -t ./fslvbm2b`
echo Running registration: ID=$fslvbm2b_id

### Creation of the GM template by averaging all (or following the template_list for) the GM_nl_0 and GM_xflipped_nl_0 images

cat <<stage_tpl3 > fslvbm2c

#!/bin/sh

if [ -f ../template_list ] ; then
    template_list=\`cat ../template_list\`
else
    template_list=\`echo *FAi.hdr | sed 's/_FAi//g'\`
    echo "WARNING - study-specific template will be created from ALL input data - may not be group-size matched!!!"
fi

template_list=\`\$FSLDIR/bin/remove_ext \$template_list\`

for g in \$template_list ; do
    mergelist="\$mergelist \${g}_FAi_GM_to_T \${g}_FAi_GM_xflipped_to_T"
done

export FSLOUTPUTTYPE=NIFTI_GZ
\$FSLDIR/bin/fslmerge -t template_4D_GM \$mergelist

export FSLOUTPUTTYPE=ANALYZE
\$FSLDIR/bin/fslmaths template_4D_GM -Tmean template_GM

stage_tpl3

chmod +x fslvbm2c
fslvbm2c_id=`fsl_sub -j $fslvbm2b_id -T 15 -N fslvbm2c ./fslvbm2c`
echo Creating template: ID=$fslvbm2c_id

echo "Study-specific template will be created, when complete, check FAi/template_4D_GM as a movie loop in fslview"

