Hi Gene,

I suspect that is not the way to go.

You are providing the FOV values on the command line, even
though they are in the DICOM file. The coordinates probably
changed because to3d still stores the DICOM transform matrix
in the HEAD file. When you changed to NIfTI, that tranform
must have been applied, even though it was different than
yours (since it would have thought they differed because one
was oblique - but it might be oblique anyway).

In any case, I think your orientation information on the
command line might be incorrect. That is the main source of
discrepancy.

Try the same command, but without any of the FOV options.
Compare the result to when you do give those options.

Note that you can still continue with the current version of
AFNI. If you want to delete the stored DICOM tranformation,
use the command:

3drefit -deoblique RAI_face1+orig

- rick