Hi Daniel,
Thank you for your reply.
Just to see that I understand you correctly..
You write: "an important point to remember is a half-voxel shift (the maximum interpolation) will introduce just as much interpolation as a seven and a half voxel shift, so you may not need to worry that much about differences between runs".
Does this mean that that after the 6 parameter (rotation/translation) rigid-body transformation, the maximal interpolation that can be introduced is 0.5 voxel in any case, independent of the initial distance in space between datasets? (I take your point regarding aligning the centers).
Best,
Uri