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#!/bin/sh
##
## Copyright 2011, 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@}
# Check for command line arguments, print help if none given
if test $# -lt 2; then
echo "Locally-weighted multi-atlas label fusion"
echo "USAGE: $0 targetImagePath atlasIntensityImage1 atlasLabelImage1 [[atlasIntensityImage2 atlasLabelImage2] ...]"
exit 2
fi
TARGET=$1
shift
ATLAS_I=""
ATLAS_L=""
while [ "$1" != "" ]; do
ATLAS_I="${ATLAS_I} $1"
ATLAS_L="${ATLAS_L} $2"
shift 2
done
echo ${ATLAS_I}
echo ${ATLAS_L}
tmpdir=`mktemp -d`
echo ${tmpdir}
idx=0
for atlas in ${ATLAS_I}; do
xfm=${tmpdir}/${idx}.xfm
${CMTK_BINARY_DIR}/registrationx --echo --init com --auto-multi-levels 5 --omit-original-data --delta-f-threshold 0.01 --dofs 6,9 --ncc --pad-ref 0 --symmetric -o ${xfm} ${TARGET} ${atlas}
idx=`expr ${idx} + 1`
done
idx=0
for atlas in ${ATLAS_I}; do
xfm=${tmpdir}/${idx}.xfm
ffd=${tmpdir}/${idx}.ffd
${CMTK_BINARY_DIR}/warpx --echo --grid-spacing 80 --grid-refine 3 --min-stepsize 0.25 --max-stepsize 16 --smoothness-constraint-weight 1e-1 --omit-original-data --delta-f-threshold 0.01 --fast --nmi -o ${ffd} --initial ${xfm} ${TARGET} ${atlas}
idx=`expr ${idx} + 1`
done
idx=0
for atlas in ${ATLAS_I}; do
ffd=${tmpdir}/${idx}.ffd
out=${tmpdir}/${idx}_i.nii
${CMTK_BINARY_DIR}/reformatx --floating ${atlas} --cubic -o ${out} ${TARGET} ${ffd}
idx=`expr ${idx} + 1`
done
lvote_inputs=""
idx=0
for atlas in ${ATLAS_L}; do
ffd=${tmpdir}/${idx}.ffd
out=${tmpdir}/${idx}_l.nii
${CMTK_BINARY_DIR}/reformatx --floating ${atlas} --pv -o ${out} ${TARGET} ${ffd}
lvote_inputs="${lvote_inputs} ${tmpdir}/${idx}_i.nii ${tmpdir}/${idx}_l.nii"
idx=`expr ${idx} + 1`
done
bin/lvote --echo -o output_${idx}_sba.nii --use-sba --patch-radius 5 ${TARGET} ${lvote_inputs}
rm -rf ${tmpdir}
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