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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: 5378 $
##
## $LastChangedDate: 2015-01-17 11:31:55 -0800 (Sat, 17 Jan 2015) $
##
## $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 distortion and subject motion in 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 coordinated:"
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 ${outdir}/dfield_fwd.nrrd
fi
unwarpedList="${b0FwdCorr}"
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 $bX"
tmpdir=$(mktemp -d)
# First, reslice using PEpolar unwarp and eddy current correction
cmtk reformatx --sinc-cosine -o ${tmpdir}/reslice.nii --pad-floating -1 --floating ${bX} ${b0FwdCorr} ${outdir}/dfield_fwd.nrrd ${xform}
# Second, multiply with Jacobian volume correction field
cmtk imagemath --in ${outdir}/jacobian.nii ${tmpdir}/reslice.nii --mul --out ${tmpdir}/reslice_j.nii
# Third, make a mask of bad slices (0 - bad slice, 1 - good slice), based on requirement that bad slices be marked as -1
cmtk convertx --float --binarize-thresh -0.5 --byte ${bX} ${tmpdir}/mask.nii
# Apply bad-slice mask back to resliced and Jacobian-corrected volume
cmtk convertx --thresh-below 0 --set-padding -1 --mask ${tmpdir}/mask.nii ${tmpdir}/reslice_j.nii ${outdir}/${base}
rm -rf ${tmpdir}
CMTK_lockfile_delete ${outdir}/${base}
fi
unwarpedList="${unwarpedList} ${outdir}/${base}"
done
##
## Motion correction
##
average=${outdir}/bAverage.nii
if CMTK_needs_update_and_lock ${average} ${b0FwdCorr} ${b0RevCorr} ${unwarpedList}; then
cmtk imagemath --in ${b0FwdCorr} ${b0RevCorr} ${unwarpedList} --average --out ${average}
CMTK_lockfile_delete ${average}
fi
for bX in ${b0FwdCorr} ${bXlist}; do
base=`basename $bX`
bXUnwarp=${outdir}/${base}
pref=`echo ${base} | sed 's/\..*//g'`
if [ "${bX}" = "${b0FwdCorr}" ]; then
if CMTK_needs_update_and_lock ${outdir}/motion/${base} ${b0FwdCorr}; then
cmtk convertx ${b0FwdCorr} ${outdir}/motion/${base}
CMTK_lockfile_delete ${outdir}/motion/${base}
fi
else
xform=${outdir}/motion/xforms/b0Unwarp_${pref}.xform
if CMTK_needs_update_and_lock ${xform} ${average} ${bXUnwarp} ; then
cmtk registrationx --pad-flt -1 --linear --dofs 6 --auto-multi-levels 3 --ncc -o ${xform} ${average} ${bXUnwarp}
CMTK_lockfile_delete ${xform}
fi
if CMTK_needs_update_and_lock ${outdir}/motion/${base} ${bXUnwarp} ${xform}; then
echo "Reformatting motion-corrected $bX"
tmpdir=$(mktemp -d)
# First, re-reslice the unwarped image
cmtk reformatx --sinc-cosine -o ${tmpdir}/reslice.nii --pad-floating -1 --floating ${bXUnwarp} ${average} ${xform}
# Second, make a mask of bad slices (0 - bad slice, 1 - good slice), based on requirement that bad slices be marked as -1
cmtk convertx --float --binarize-thresh -0.5 ${bX} ${tmpdir}/mask.nii
# Third, reslice the mask using the same motion xform and interpolation as the image
cmtk reformatx --sinc-cosine -o ${tmpdir}/mask_reslice.nii --floating ${tmpdir}/mask.nii ${average} ${xform}
# Fourth, threshold resliced mask to include only those pixels that have more then 50% support
cmtk convertx --binarize-thresh 0.5 ${tmpdir}/mask_reslice.nii ${tmpdir}/mask_thresh.nii
# Fifth, create final image by masking out pixels with under 50% support
cmtk convertx --set-padding -1 --mask ${tmpdir}/mask_thresh.nii --thresh-below 0 ${tmpdir}/reslice.nii ${outdir}/motion/${base}
rm -rf ${tmpdir}
CMTK_lockfile_delete ${outdir}/motion/${base}
fi
fi
done
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