Thanks @epnev! That clarifies about the iterations. That makes sense to me about the error. I currently am rigidly registering the whole volume initially to align the z-planes (there is a bit of movement in Z) and then non-rigidly aligning each plane independently using a grid size of [64,64], max_shifts 15, overlap_pre [16,16], overlap_post [8,8], max_dev [4,4]. The recording size varies but is around 200x200. I've tried varying these a bit and reducing the max_shifts from 20 -> 15 helped some, also it seemed like increasing overlap_post to [16,16] helped. Is there a good rule of thumb to help choose these?