Hi, Ben-
THanks, with the 3dinfo I was trying to get a sense of whether the voxel sizes were changing dramatically or something.
With the 2nd 3dAllineate, I don't htink you need/want both "-base .." and "-master ..".
I'm not sure what's happening. I will PM you instructions so you can upload the dset and I can take a look more directly on this side, if that works for you.
-pt