Showing black border square when conducting affine transform

pyushkevich / greedy

Very fast greedy diffeomorphic registration code

GNU General Public License v3.0

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Showing black border square when conducting affine transform #11

Open AndysonYs opened 4 years ago

AndysonYs commented 4 years ago

147 like above(one slice of a 3d picture) Is there anything wrong with the parameters? Here is the .bash file I use. All the .nii file are 3 dimensional picture. 001_Cta.nii is fixed. 2.nii is moved. ~/Greedy/build/greedy -d 3 -a \ -i ./CTAs/001_Cta.nii ./CTAs/2.nii \ -ia-image-centers \ -o affine.mat \ -n 100x50x0 \ -m NCC 2x2x2

~/Greedy/build/greedy -d 3 \ -rf ./CTAs/001_Cta.nii \ -rm ./CTAs/2.nii resliced.nii \ -ri LABEL 0.2vox \ -r affine.mat

cookpa commented 4 years ago

I think this happens because any voxels in the in the output that are outside the moving image domain are set to a default value. This is usually 0, but for CT that might not be the right background value. You can change this by adding -rb <value> to your reslicing call.