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#!/bin/sh
##
## Copyright 1997-2009 Torsten Rohlfing
##
## Copyright 2004-2012, 2014 SRI International
##
## This file is part of the Computational Morphometry Toolkit.
##
## http://www.nitrc.org/projects/cmtk/
##
## The Computational Morphometry Toolkit is free software: you can
## redistribute it and/or modify it under the terms of the GNU General Public
## License as published by the Free Software Foundation, either version 3 of
## the License, or (at your option) any later version.
##
## The Computational Morphometry Toolkit is distributed in the hope that it
## will be useful, but WITHOUT ANY WARRANTY; without even the implied
## warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License along
## with the Computational Morphometry Toolkit. If not, see
## <http://www.gnu.org/licenses/>.
##
## $Revision: 5337 $
##
## $LastChangedDate: 2014-04-30 13:22:51 -0700 (Wed, 30 Apr 2014) $
##
## $LastChangedBy: torstenrohlfing $
##
export CMTK_BINARY_DIR=${CMTK_BINARY_DIR:-@CMTK_BINARY_DIR_CONFIG@}
# Get the cmtk_functions.sh script from the scripts/ directory in the CMTK source tree
. ${CMTK_BINARY_DIR}/cmtk_functions.sh
# Check for command line arguments, print help if none given
if test $# -lt 2; then
echo "Correct multiple-NEX image motion"
echo "USAGE: $0 outImagePath referenceImagePath imageNEX1 [...]"
exit 2
fi
tmpdir=`mktemp -d`
if [ "${tmpdir}" = "" ]; then
echo "ERROR: cannot create tmpdir"
exit
fi
outfile=$1
reffile=$2
shift 2
fltfiles="$*"
images=${reffile}
for f in ${fltfiles}; do
name=`basename ${f}`
echo "Registration: ${name}"
xform=${tmpdir}/${name}.list
cmtk registration -i -o ${xform} -a 0.01 --dofs 6 -e 2 ${reffile} ${f}
echo "Reformatting: ${name}"
nrrd=${tmpdir}/reformat/${name}.nrrd
cmtk reformatx --sinc-cosine --sinc-window-width 5 -o ${nrrd} --floating ${f} ${reffile} ${xform}
images="${images} ${nrrd}"
done
echo "Averaging"
cmtk average_images -o ${outfile} ${images}
echo "Done."
rm -rf ${tmpdir}
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