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#!/bin/bash
NUMPARAMS=$#
if [ $NUMPARAMS -lt 2 ]
then
echo " USAGE :: "
echo " sh geodesicinterpolation.sh image1 image2 N-interpolation-points N-step-size Use-Affine-Initialization? Mask-Image Auxiliary-Template "
echo " N-interpolation-points -- if you choose 10 points and step-size of 1 then you will get 8 interpolated/morphed images -- end-points are the original images "
echo " if you choose 10 points and step-size of 2 then you will get 4 interpolated/morphed images -- end-points are the original images "
echo " if you use affine initialization - sometimes it could cause unpleasantness, if the affine mapping is large -- sometimes it may be needed, though "
echo " the mask image restricts matching to an ROI "
echo " The Auxiliary-Template is another image through which the morph images (image1 and image2) are mapped -- this often helps, if the auxiliary template is an average face image "
echo " "
echo " You may need to tune the ANTS parameters coded within this script for your application "
exit
fi
# should we use the generative model to find landmarks then
# drive individual mappings by the LMs?
TEMPLATE=$1
TARGET=$2
NUMSTEPS=10
STEP=1
OUTNAME=ANTSMORPH
if [ $NUMPARAMS -gt 2 ]
then
NUMSTEPS=$3
fi
if [ $NUMPARAMS -gt 3 ]
then
STEP=$4
fi
USEAFF=0
if [ $NUMPARAMS -gt 4 ]
then
USEAFF=$5
fi
MASK=0
if [ $NUMPARAMS -gt 5 ]
then
MASK=$6
fi
TEMPLATEB=0
if [ $NUMPARAMS -gt 6 ]
then
TEMPLATEB=$7
fi
echo " Morphing in total $NUMSTEPS time-points by $STEP steps -- end-points are original images "
echo " Use-Affine ? $USEAFF "
echo " templateB $TEMPLATEB "
for (( n = 0 ; n <= ${NUMSTEPS}; n=n+${STEP} ))
do
BLENDINGA=$(echo "scale=2; ${n}/${NUMSTEPS}" | bc )
BLENDINGB=$(echo "scale=2; 1-$BLENDINGA" | bc )
BLENDNAME=$(echo "scale=2; 100*$BLENDINGA" | bc )
echo " Blending values: $BLENDINGA and $BLENDINGB"
done
ITS=100x100x10
TRAN=SyN[0.5]
REG=Gauss[3,1]
RADIUS=6
if [ $NUMPARAMS -le 5 ]
then
if [ $USEAFF -eq 0 ]
then
ANTS 2 -m PR[ $TEMPLATE,$TARGET,1,${RADIUS}] -t $TRAN -r $REG -o $OUTNAME -i $ITS --number-of-affine-iterations 0 -x $MASK
fi
if [ $USEAFF -ne 0 ]
then
ANTS 2 -m PR[ $TEMPLATE,$TARGET,1,${RADIUS}] -t $TRAN -r $REG -o $OUTNAME -i $ITS -x $MASK #--MI-option 16x2000
fi
ComposeMultiTransform 2 ${OUTNAME}Warp.nii.gz -R $TEMPLATE ${OUTNAME}Warp.nii.gz ${OUTNAME}Affine.txt
ComposeMultiTransform 2 ${OUTNAME}InverseWarp.nii.gz -R $TARGET -i ${OUTNAME}Affine.txt ${OUTNAME}InverseWarp.nii.gz
fi
if [ $NUMPARAMS -gt 5 ]
then
if [ $USEAFF -eq 0 ]
then
#echo " Pseudo-Morphing "
#echo " method 1 "
ANTS 2 -m PR[ $TEMPLATEB,$TARGET,1,${RADIUS}] -t $TRAN -r $REG -o ${OUTNAME}B -i $ITS --number-of-affine-iterations 0 -x $MASK
ANTS 2 -m PR[ $TEMPLATE,$TEMPLATEB,1,${RADIUS}] -t $TRAN -r $REG -o ${OUTNAME}A -i $ITS --number-of-affine-iterations 0 -x $MASK
ComposeMultiTransform 2 ${OUTNAME}AWarp.nii.gz -R $TEMPLATE ${OUTNAME}AWarp.nii.gz ${OUTNAME}AAffine.txt
ComposeMultiTransform 2 ${OUTNAME}AInverseWarp.nii.gz -R $TEMPLATEB -i ${OUTNAME}AAffine.txt ${OUTNAME}AInverseWarp.nii.gz
ComposeMultiTransform 2 ${OUTNAME}BWarp.nii.gz -R $TEMPLATEB ${OUTNAME}BWarp.nii.gz ${OUTNAME}BAffine.txt
ComposeMultiTransform 2 ${OUTNAME}BInverseWarp.nii.gz -R $TARGET -i ${OUTNAME}BAffine.txt ${OUTNAME}BInverseWarp.nii.gz
ComposeMultiTransform 2 ${OUTNAME}Warp.nii.gz -R $TEMPLATE ${OUTNAME}AWarp.nii.gz ${OUTNAME}BWarp.nii.gz
ComposeMultiTransform 2 ${OUTNAME}InverseWarp.nii.gz -R $TARGET ${OUTNAME}BInverseWarp.nii.gz ${OUTNAME}AInverseWarp.nii.gz
#
#echo " method 2 "
#ComposeMultiTransform 2 ${OUTNAME}Warp.nii.gz -R $TEMPLATE ${OUTNAME}AWarp.nii.gz ${OUTNAME}AAffine.txt ${OUTNAME}BWarp.nii.gz ${OUTNAME}BAffine.txt
#ComposeMultiTransform 2 ${OUTNAME}InverseWarp.nii.gz -R $TARGET -i ${OUTNAME}BAffine.txt ${OUTNAME}BInverseWarp.nii.gz -i ${OUTNAME}AAffine.txt ${OUTNAME}AInverseWarp.nii
#
fi
if [ $USEAFF -ne 0 ]
then
#echo " Pseudo-Morphing "
#echo " method 1 "
ANTS 2 -m PR[ $TEMPLATEB,$TARGET,1,${RADIUS}] -t $TRAN -r $REG -o ${OUTNAME}B -i $ITS -x $MASK
ANTS 2 -m PR[ $TEMPLATE,$TEMPLATEB,1,${RADIUS}] -t $TRAN -r $REG -o ${OUTNAME}A -i $ITS -x $MASK
ComposeMultiTransform 2 ${OUTNAME}AWarp.nii.gz -R $TEMPLATE ${OUTNAME}AWarp.nii.gz ${OUTNAME}AAffine.txt
ComposeMultiTransform 2 ${OUTNAME}AInverseWarp.nii.gz -R $TEMPLATEB -i ${OUTNAME}AAffine.txt ${OUTNAME}AInverseWarp.nii.gz
ComposeMultiTransform 2 ${OUTNAME}BWarp.nii.gz -R $TEMPLATEB ${OUTNAME}BWarp.nii.gz ${OUTNAME}BAffine.txt
ComposeMultiTransform 2 ${OUTNAME}BInverseWarp.nii.gz -R $TARGET -i ${OUTNAME}BAffine.txt ${OUTNAME}BInverseWarp.nii.gz
ComposeMultiTransform 2 ${OUTNAME}Warp.nii.gz -R $TEMPLATE ${OUTNAME}AWarp.nii.gz ${OUTNAME}BWarp.nii
ComposeMultiTransform 2 ${OUTNAME}InverseWarp.nii.gz -R $TARGET ${OUTNAME}BInverseWarp.nii.gz ${OUTNAME}AInverseWarp.nii.gz
#
#echo " method 2 "
#ComposeMultiTransform 2 ${OUTNAME}Warp.nii.gz -R $TEMPLATE ${OUTNAME}AWarp.nii.gz ${OUTNAME}AAffine.txt ${OUTNAME}BWarp.nii.gz ${OUTNAME}BAffine.txt
#ComposeMultiTransform 2 ${OUTNAME}InverseWarp.nii.gz -R $TARGET -i ${OUTNAME}BAffine.txt ${OUTNAME}BInverseWarp.nii.gz -i ${OUTNAME}AAffine.txt ${OUTNAME}AInverseWarp.nii
#
fi
fi
for (( n = 0 ; n <= ${NUMSTEPS}; n=n+${STEP} ))
do
BLENDINGA=$(echo "scale=2; ${n}/${NUMSTEPS}" | bc )
BLENDINGB=$(echo "scale=2; 1-$BLENDINGA" | bc )
BLENDNAME=$(echo "scale=2; 100*$BLENDINGA" | bc )
echo " Blending values: $BLENDINGA and $BLENDINGB"
BASEA=${TEMPLATE%.*}
BASEB=${TARGET%.*}
MultiplyImages 2 ${OUTNAME}InverseWarp.nii.gz $BLENDINGA SM${OUTNAME}InverseWarp.nii.gz
MultiplyImages 2 ${OUTNAME}InverseWarp.nii.gz $BLENDINGA SM${OUTNAME}InverseWarp.nii.gz
MultiplyImages 2 ${OUTNAME}Warp.nii.gz $BLENDINGB SM${OUTNAME}Warp.nii.gz
MultiplyImages 2 ${OUTNAME}Warp.nii.gz $BLENDINGB SM${OUTNAME}Warp.nii.gz
WarpImageMultiTransform 2 $TARGET temp.nii.gz SM${OUTNAME}Warp.nii.gz -R $TEMPLATE
ImageMath 2 temp.nii.gz Normalize temp.nii.gz 1
ImageMath 2 temp.nii.gz m temp.nii.gz 1. #$BLENDINGA
WarpImageMultiTransform 2 $TEMPLATE temp2.nii.gz SM${OUTNAME}InverseWarp.nii.gz -R $TEMPLATE
ImageMath 2 temp2.nii.gz Normalize temp2.nii.gz 1
ImageMath 2 temp2.nii.gz m temp2.nii.gz 0 #$BLENDINGB
echo " ImageMath 2 ${BASEA}${BASEB}${BLENDNAME}morph.nii.gz + temp2.nii.gz temp.nii.gz "
ImageMath 2 ${BASEA}${BASEB}${BLENDNAME}morph.nii.gz + temp2.nii.gz temp.nii.gz
ConvertToJpg ${BASEA}${BASEB}${BLENDNAME}morph.nii.gz ${BASEA}${BASEB}${BLENDNAME}morph.jpg
rm -f ${BASEA}${BASEB}${BLENDNAME}morph.nii.gz
done
rm -f ${OUTNAME}* SM${OUTNAME}*
exit
|
