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antsRegistrationCommandDiffeomorphismTest.sh
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antsRegistrationCommandDiffeomorphismTest.sh
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fixedPoints='data/pointsLowerLeft.nii.gz'
movingPoints='data/pointsUpperRight.nii.gz'
ImageMath 2 data/pointsLowerLeftP.nii.gz PadImage \
$fixedPoints 50
ImageMath 2 data/pointsUpperRightP.nii.gz PadImage \
$movingPoints 50
fixedPoints='data/pointsLowerLeftP.nii.gz'
movingPoints='data/pointsUpperRightP.nii.gz'
outputDirectory='./'
outputPrefix=${outputDirectory}/diffeomorphismTest
s=1 # sampling rate
k=5 # k - neighborhood
txs="SyN[0.25,6,0.0]"
txb="BSplineSyN[0.2,2x2,0,5]"
tx=$txb
time antsRegistration -d 2 \
-o ${outputPrefix} \
-x [${fixedPoints},${movingPoints}] \
-m PSE[${fixedPoints},${movingPoints},1,${s},0,50,$k] \
-t $tx \
-c [200x200x200x200x50,0,10] \
-s 0x0x0x0x0 \
-f 8x8x4x2x1
antsApplyTransforms -d 2 \
-o ${outputPrefix}Warped.nii.gz \
-i ${movingPoints} \
-r ${fixedPoints} \
-n NearestNeighbor \
-t ${outputPrefix}0Warp.nii.gz
#
antsApplyTransforms -d 2 \
-o ${outputPrefix}InvWarped.nii.gz \
-i ${fixedPoints} \
-r ${movingPoints} \
-n NearestNeighbor \
-t ${outputPrefix}0InverseWarp.nii.gz
ImageMath 2 ${outputPrefix}invid.nii.gz InvId ${outputPrefix}0InverseWarp.nii.gz ${outputPrefix}0Warp.nii.gz
CreateWarpedGridImage 2 ${outputPrefix}0Warp.nii.gz ${outputPrefix}Grid.nii.gz
CreateWarpedGridImage 2 ${outputPrefix}0InverseWarp.nii.gz ${outputPrefix}InvGrid.nii.gz
# now visualize with snap
# snap -g diffeomorphismTestGrid.nii.gz -s diffeomorphismTestWarped.nii.gz