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antsRegistrationCommandCirclexSquare.sh
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antsRegistrationCommandCirclexSquare.sh
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fixedPoints='data/circles.nii.gz'
movingPoints='data/squares.nii.gz'
outputDirectory='./'
outputPrefix=${outputDirectory}/circlesxSquares
s=1 # sampling rate
k=10 # k - neighborhood
antsRegistration -d 2 -v 1 \
-o ${outputPrefix} \
-x [${fixedPoints},${movingPoints}] \
-r [${fixedPoints},${movingPoints},1] \
-m PSE[${fixedPoints},${movingPoints},1,${s},1,20,$k] \
-t Affine[0.1] \
-c [50,0,10] \
-s 0 \
-f 1 \
-m PSE[${fixedPoints},${movingPoints},1,${s},1,10,$k] \
-t Affine[0.1] \
-c [40,0,10] \
-s 0 \
-f 1 \
-m PSE[${fixedPoints},${movingPoints},1,${s},1,5,$k] \
-t Affine[0.1] \
-c [20,0,10] \
-s 0 \
-f 1 \
-m PSE[${fixedPoints},${movingPoints},1,${s},1,20,$k] \
-t SyN[0.2,6,0] \
-c [100x100x100,0,10] \
-s 0x0x0 \
-f 3x2x1
antsApplyTransforms -d 2 -v 1 \
-o ${outputPrefix}Warped.nii.gz \
-i ${movingPoints} \
-r ${fixedPoints} \
-n NearestNeighbor \
-t ${outputPrefix}1Warp.nii.gz \
-t ${outputPrefix}0GenericAffine.mat