Hello @Dodox,
OK, it looks like my hunch was wrong and it is not early termination due to small number of iterations. One thing that I am not sure of with the image you provided is with respect to the registration errors as it is hard to judge based on the fused images.
As a first step, can you try a manual registration and evaluation of that registration as shown in this notebook section titled Register using manual initialization. I am not sure if the MR images are not 180 degrees from each other as in the images you provided the head is almost spherical (easy to identify gross errors in slices that include the nose/eyes).