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Showing black border square when conducting affine transform #11

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AndysonYs opened this issue Aug 6, 2019 · 1 comment
Open

Showing black border square when conducting affine transform #11

AndysonYs opened this issue Aug 6, 2019 · 1 comment

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@AndysonYs
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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
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cookpa commented Aug 15, 2019

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.

pyushkevich pushed a commit that referenced this issue Dec 28, 2024
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