Hi Linda,

It is not clear why you are not using afni_proc.py for
the first level analysis. To do so, add the surf block
and the -surf_anat and -surf_spec options to a typical
afni_proc.py volumetric analysis command, where the
spec file should be fore the standard mesh surfaces.


Ignoring that, consider using the standard mesh
surfaces directly in the 3dVol2Surf command. There
is probably no reason to use the original surfaces once
the standard mesh ones exist.

Also, 3dWarp -deoblique is is generally not necessary
before running 3dvolreg or align_epi_anat.py. Again,
it might be a very good idea to look at what afni_proc.py
would do.

Consider "Example 8" from the "afni_proc.py -help" output.

Also, consider the sample scripts from the class data,
including the afni_proc.py command script in
AFNI_data6/FT_analysis/s03.ap.surface,
as well as the corresponding analysis script,
AFNI_data6/FT_analysis/s13.proc.FT.surf.

Writing your own scripts is a great way to learn.
But it may be a good idea to try afni_proc.py for
the actual analysis. At least try it and compare.

- rick