Thanks for the quick response. I've played around with the 3drefit command, and it definitely seems to be what I'm looking for; however, no matter what I try, I can't seem to make the orientation of the datasets line up.

The original anatomical dataset that I reconstruct from DICOM to AFNI is in RSA orientation.
When I transform the anatomical dataset from AFNI to ANALYZE, I use the -orient LPI command. Using 3dcopy to get the traced ROI dataset back into AFNI, the orientation remains LPI.

At this point, despite the fact that the original anatomical dataset is in RSA orientation and the traced ROI dataset is in LPI orientation, both appear to be in the same orientation in the AFNI viewer; it is just the alignment that is slightly off. This in itself seems a bit odd....?

With the -duporigin command, the alignment becomes much much worse (presumably because of the different orientations?). And when I try to orient the traced ROI dataset to that of the original anatomical (RSA), it ends up upside down and face down. Playing around with the -orient command and the -xorigin, -yorigin, and -zorigin commands in 3drefit, I am able to get the R to L extent, A to P extent, and I to S extent to match between the two datasets, but I can't seem to make the orientations of the two datasets match.

Not sure where to go from here, but any advice/help would be great!!

Thanks again,
L