Hi Wolfgang

> I'm using Freesurfer to generate surfaces, and after running
> the SUMA_Make_Spec_FS script I end up having 2 separate spec
> files for the right and left hemisphere.
>
> I'm wondring what the suggested way is to have them both in the
> surface viewer at the same time and mapping FMRI activation to
> it:
>
> To view them together I created a combined spec file, where I
> just pasted the surface entries of the other hemisphere at the
> end (without any further changes).
That's fine. You might want to give the inflated surfaces different states so that they do not get displayed together. I take it you know about the '[' and ']' keys in SUMA... Take a look at the spec file N27_both.spec that is distributed with SUMA's N27 surfaces ( [afni.nimh.nih.gov] ) for detail.


> Then I use The Vol2Surf plugin to visualize my FMRI activation
> on the surface. I'd like to see the maximum between the
> smoothed white matter and pial surface.
>
> As I have both hemispheres at once I set surf_pair0 to surf_A=0
> and surf_B=1, and surf_pair_1 to surf_A=3 and surf_B=4.
>
> The debug output tells me:
> +d surf_A label: 'lh.smoothwm.asc'
> +d surf_B label: 'lh.pial.asc'
> +d surf_A label: 'rh.smoothwm.asc'
> +d surf_B label: 'rh.pial.asc'
>
> Question 2) Is this the right way to use the surf_pair settings
> in Vol2Surf when having both hemispheres at the same time (like
> elaborated above)?
>
That seems good. You could run SUMA with just one pair or command-line 3dVol2Surf to make sure all is well.

> Thanks much,
> Wolfgang
>
cheers,
-ziad