Hi @ptrblck
I performed the equality test on a CT image by padding, creating non-overlapping patches and reconstructing it back. The patches were correctly located.
I did the following:

Padded the MR and CT images to the size of multiples of 32.
Took the non-overlapping patches and created the test dataset.
From the output reconstructed the image by connecting the patches.

But the same mismatches are found:

image.png661×649 75 KB

What might be the reason, am I not training the network enough? or shall I try overlapping patches and do intensity averaging in overlapping regions?