Hi Joel,

Ah, that makes sense.

There are 2 or three steps to the warp, and I do not
know exactly how they are used (in the matrices).

1. orig->acpc shift/rotation
2. orig->acpc resample to 1.0 mm^3 in RAI orientation
3. acpc->tlrc 12 piece transformation

So do you apply any warp/translation/rotation/re-grid
on the tlrc dataset when it is in your Pittsburgh MRI
format? If not, it may be best to try to leave the WARP
matrices as they are.

In either case, it seems to me that you should be able
to use the tlrc dataset for -apar, particularly if you
use the version _before_ conversion to P-MRI format.

As a second possibility, and one you may have to consider
anyway (to match grids), try using "3dresample -orient RAI"
(or "-master preMRI+tlrc") on the post-P-MRI dataset. It
might then be okay to use it as the -apar dataset (that
would need testing).

I guess I'm hoping that the RAS orientation is the problem...

- rick