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#!/bin/bash
##
## Copyright 2009-2010, 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 "Iterative Shape Averging"
echo "USAGE: $0 referenceImagePath imagePath1 imagePath2 ..."
echo " where the first argument is the path of the initial reference image and"
echo " the remaining arguments are the remaining images in the set to be averaged."
echo " Please make sure the initial reference image is not also listed in the"
echo " list of remaining images."
exit 2
fi
# We should have received a list of all images via the command line
IMAGES="$*"
# Warp arguments common to all iterations
WARP_ARGS_GLOBAL="--echo -v --refine 1 --delay-refine --energy-weight 1e-1"
# This function computed the average of reformatted images.
average_images()
{
local out_img=$1
shift
local in_imgs="$*"
if CMTK_needs_update_and_lock ${out_img} ${in_imgs}; then
cmtk average_images --echo -o ${out_img} ${in_imgs}
CMTK_lockfile_delete ${out_img}
fi
}
# This function will compute the affine alignments of one image to the initial reference.
pass0()
{
local images="$*"
local in_ref=$1
local out_nii_list=""
local ref_name=`basename ${in_ref} | sed 's/\..*//g'`
for in_flt in ${images}; do
local flt_name=`basename ${in_flt} | sed 's/\..*//g'`
local out_xfm=isa/pass0/${flt_name}.xform
if CMTK_needs_update_and_lock ${out_xfm} ${in_ref} ${in_flt}; then
if [ "${in_ref}" != "${in_flt}" ]; then
cmtk registration --echo --initxlate --auto-multi-levels 5 -v --dofs 6 --dofs 9 -o ${out_xfm} ${in_ref} ${in_flt}
else
cmtk make_initial_affine --identity ${in_ref} ${in_flt} ${out_xfm}
fi
CMTK_lockfile_delete ${out_xfm}
fi
local out_nii=isa/pass0/${flt_name}.nii
out_nii_list="${out_nii_list} ${out_nii}"
if CMTK_needs_update_and_lock ${out_nii} ${out_xfm}; then
cmtk reformatx --echo --sinc-cosine -o ${out_nii} --floating ${in_flt} ${in_ref} ${out_xfm}
CMTK_lockfile_delete ${out_nii}
fi
done
average_images isa/pass0/average.nii ${out_nii_list}
}
# Determine warp arguments from iteration number and reference image
get_level_warp_args()
{
local iteration=$1
local initial_ref=$2
local cpspacing=`cmtk describe --machine-readable ${initial_ref} | fgrep FOV | cut -f2 | cmtk sequence | fgrep STATval | cut -f2`
for ((i=1;i<iteration;++i)); do
cpspacing=`echo ${cpspacing} | gawk '{print $1 / 2}'`
done
local warp_args="${WARP_ARGS_GLOBAL} --grid-spacing ${cpspacing}"
echo ${warp_args}
}
# This function computes the subsequent rounds of nonrigid alignments.
passn()
{
local curr=$1
local prev=`expr ${curr} - 1`
shift
local images="$*"
local initial_ref=$1
local out_nii_list=""
local ref_nii=isa/pass${prev}/average.nii
local warp_args=`get_level_warp_args ${curr} ${initial_ref}`
for in_flt in ${images}; do
local flt_name=`basename ${in_flt} | sed 's/\..*//g'`
local out_xfm=isa/pass${curr}/${flt_name}.xform
local inp_xfm=isa/pass${prev}/${flt_name}.xform
if CMTK_needs_update_and_lock ${out_xfm} ${inp_xfm} ${ref_nii} ${in_flt}; then
cmtk warp ${warp_args} --initial ${inp_xfm} -o ${out_xfm} ${ref_nii} ${in_flt}
CMTK_lockfile_delete ${out_xfm}
fi
local out_nii=isa/pass${curr}/${flt_name}.nii
out_nii_list="${out_nii_list} ${out_nii}"
if CMTK_needs_update_and_lock ${out_nii} ${out_xfm}; then
cmtk reformatx --echo --sinc-cosine -o ${out_nii} --floating ${in_flt} ${ref_nii} ${out_xfm}
CMTK_lockfile_delete ${out_nii}
fi
done
average_images isa/pass${curr}/average.nii ${out_nii_list}
}
# Run the iterative procedure
pass0 ${IMAGES}
for n in 1 2 3 4 5; do
passn ${n} ${IMAGES}
done
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