Hi Brianna,

I am quite surprised that the output changes at all using
3dresample -orient. It should end up on the same grid, and
result in the same values, exactly.

Also since spmT_0001.hdr is an ANALYZE dataset, I'm surprised
that AFNI would think it's LAI. Unless you have an environment
variable telling AFNI to assume ANALYZE datasets are in LAI
orientation, it should default to expecting them in LPI.

In general, AFNI cannot tell what the orientation is, since
that is not a reliable part of the ANALYZE header.

---

In any case, what you want to do is not actually change the
orientation of the data via 3dresample (which involves moving
the data around), but to tell AFNI to just think that it's a
different orientation.

Since it was not created with the correct orientation, it must
be changed using 3drefit -orient. That will modify the text
in the .HEAD file, but not the data in the .BRIK file.

---

If you do not know the orientation, try what it was before
you changed it to ANALYZE format in the first place. If it was
LPI then, use LPI now.

3drefit -orient LPI spmT_0001+orig


- rick