Applying affine transform to label image in ITK

I did affine transformation between Moving and Fixed images. My moving image has label image too. After finding the transformation, I want to apply it to the label image of moving image and get the label for fixed image.
For the images that are of similar intensities and taken from the same scanner, I am able to transfer the label. Why is it not happening for the images taken on different scanners?
I’m using NNinterpolator right now.

If you do registration correctly, and use resample filter, it should not matter whether images came from the same scanner or from different modalities. Double check that the label map perfectly overlays the image you are registering to (by visualizing them in Slicer). Also double check you are applying the transform in the correct direction (direct or inverse).

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