In my experience an initial failure to get the "pose" correct is the most common cause of failure for otherwise reasonable quality images. You can check if this by looking at the translation/rotation/scale etc parameters in the `registration` output file. You can get round this by providing an initial affine registration that roughly aligns things. If you have very standardised images it may be possible to provide a standard initialisation procedure which is more robust than the default. All the best, Greg.