Hi Dan,

1) It might not be advantageous to convert to MNI space
before running FreeSurfer. In order to do the group
analysis on the surface, you would need to use the standard
mesh surfaces, and those go through FreeSurfer's registration
to their own template (on the surface).

The prior volumetric transformation will distort and smooth
the anatomical before FreeSurfer see it. I am not sure how
that might affect the results.


Usually surface analysis is done in orig space, though the
standard mesh surfaces are immediately usable in group
analysis. Then one can use the surface from the anatomical
template for reference, which will give MNI coordinates to
those surface nodes.

But still, what you are doing should work, assuming you ran
FreeSurfer on the MNI space subject anat datasets.


2) Yes, smoothing should be done on the surface. That is
one of the main advantages of running a surface analysis.
Scaling does not matter, except with regard to the order
of processing steps.

- rick