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#!/bin/sh
##
## Copyright 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 $
##
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 distortion of diffusion-weighted MR images."
echo
echo "For this script to be applicable, the b=0 image must have been acquired twice, "
echo "once with standard phase encoding direction and once with phase encoding reversed."
echo
echo "USAGE: $0 outdir b0Reverse b0Forward bX1 [bX2 ...]"
exit 2
fi
outdir=$1
b0Rev=$2
b0Fwd=$3
if ! cmtk geomatch -v ${b0Rev} ${b0Fwd}; then
echo "ERROR: the two b=0 images have mismatched geometries or spatial coordinates:"
echo " ${b0Rev}"
echo " ${b0Fwd}"
exit 1
fi
shift 3
bXlist="$*"
#
# First, do eddy currents by registering all bX images to forward b=0 image
#
for bX in ${bXlist}; do
base=`basename $bX`
pref=`echo ${base} | sed 's/\..*//g'`
xform=${outdir}/eddy/b0_${pref}.xform
if CMTK_needs_update_and_lock ${xform} ${b0Fwd} ${bX}; then
echo "Computing eddy current correction for ${base}..."
cmtk registrationx --pad-flt -1 --restrict-in-plane xy --cubic --dofs 9,12 --auto-multi-levels 2 --nmi -o ${xform} ${b0Fwd} ${bX}
CMTK_lockfile_delete ${xform}
fi
done
b0FwdCorr=${outdir}/`basename ${b0Fwd}`
b0RevCorr=${outdir}/`basename ${b0Rev}`
if CMTK_needs_update_and_lock ${outdir}/dfield_fwd.nrrd ${b0Fwd} ${b0Rev}; then
echo "Computing deformation..."
cmtk epiunwarp --no-flip --write-jacobian-fwd ${outdir}/jacobian.nii --smooth-sigma-max 16 --smooth-sigma-min 0 --smooth-sigma-diff 0.25 --iterations 5 --smoothness-constraint-weight 1e4 --phase-encode-ap ${b0Fwd} ${b0Rev} ${b0FwdCorr} ${b0RevCorr} ${outdir}/dfield_fwd.nrrd
CMTK_lockfile_delete ${outdir}/dfield_fwd.nrrd
fi
for bX in ${bXlist}; do
base=`basename $bX`
pref=`echo ${base} | sed 's/\..*//g'`
xform=${outdir}/eddy/b0_${pref}.xform
if CMTK_needs_update_and_lock ${outdir}/${base} ${bX} ${outdir}/dfield_fwd.nrrd ${xform}; then
echo "Unwarping $bX"
cmtk reformatx --sinc-cosine -o ${outdir}/${base} --pad-floating -1 --floating ${bX} ${b0FwdCorr} ${outdir}/dfield_fwd.nrrd ${xform} && cmtk imagemath --in ${outdir}/jacobian.nii ${outdir}/${base} --mul --out ${outdir}/${base}
CMTK_lockfile_delete ${outdir}/${base}
fi
done
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