Hi Dan,

The impression that I had (though was not sure about,
and so mentioned it as an assumption) was that you ran
FreeSurfer on standard space anatomical volumes.

Since that is not true, and you are running FS on orig
data, then it is preferable to no run AlignToExperiment
using standard space data. It is not horrible if the
alignment is affine, but non-linear cannot be done.


It seems to me then there is no reason to go to standard
space. Consider following the class analysis example
that starts with orig space surfaces.

There is an afni_proc.py command: AFNI_data6/FT_analysis/s03.ap.surface
and the corresponding proc script: AFNI_data6/FT_analysis/s13.proc.FT.surf

@SUMA_AlignToExperiment is run in there.

- rick