Greetings,

I'm the main author of CoSMoMVPA. Hopefully my responses below are helpful.

herrlich10 Wrote:
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> I'm using AFNI/FreeSurfer/SUMA tool chain, and
> CoSMoMVPA matlab package to do surface-based MVPA,
> and encountered a few problems. Any help would be
> highly appreciated.
>
> 1) According to the CoSMoMVPA demo, its
> surface-based searchlight routine seems to require
> merged hemisphere (mh, as opposed to lh+rh) format
> of the FS surface (in *.asc file). However,
> @SUMA_Make_Spec_FS generates separated (lh+rh)
> files. I used the following pseudo matlab code to
> merge the two:
> [left_verts, left_faces] =
> s] = read_asc('lh.asc');
> [right_verts, right_faces] =
> s] = read_asc('rh.asc');
> right_faces(:,1:3) = right_faces(:,1:3) +
> 3) + size(left_verts,1);
> write_asc('mh.asc', [left_verts; right_verts],
> ts], [left_faces; right_faces]);
> It seemed to work (but is it the correct way to do
> this?).

Yes, that should be fine.

> But when I visualize the merged surfaces,
> I realized that the spatial location of the
> vertices from the two hemispheres in volumetric
> space are overlaped. Is that OK?

You can add an offset to the coordinates, for example to the first column in left_verts and right_verts to add or subtract some value from the x coordinate.

> Specifically,
> will that affect neighborhood definition or
> multiple comparison correction?

It should not really, as neighborhoods are defined through the faces. So even if surfaces from two hemispheres overlap spatially, there are no two nodes with one in each hemisphere that are neighbors.

> 2) After I got the surface-based searchlight
> result with CoSMoMVPA in a *.niml.dset file, which
> contains the results for both hemispheres, I tried
> to load and visualize it with SUMA. However, with
> SUMA object controller, I could load the dset onto
> only one of the two hemispheres (either left or
> right, but not both). When I loaded the same dset
> to the second hemisphere, SUMA complained and
> failed.
> Is there a way to visualize merged hemisphere dset
> with SUMA?

It should work fine to load the merged hemisphere directly (i.e. using an mh.asc file as you defined earlier). It may require a custom .spec file that points to the merged hemisphere files, not left or right hemispheres. How does SUMA complain?

As a side note: PyMVPA's pymvpa2-prep-afni-surf is a script that helps with merging hemispheres, writing spec files, and more. It takes as input the result from FreeSurfer's recon-all. See [www.pymvpa.org] for details.