tobiamj Wrote:
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> Dear Ziad and Afni Experts,
>
> I'm trying to compare cortical thickness for the
> affected hemisphere of a patient group to their
> unaffected hemisphere (the affected hemisphere is
> sometimes left and sometimes right, so it requires
> surface node/vertex symmetery). Is it possible to
> use SUMA_Make_Spec_FS to generate a SUMA surface
> from the lh.rh.sphere.reg (it's the output from
> freesurfer's recon-all with -contrasurfreg flag) ?
> I've already converted the .reg surface to .asc
> using mris_convert, but then running the make_spec
> does not seem to recognize/convert it to niml
> format as it does for ipsilateral surfaces.

Hi Michael,

I have never used the lh.rh.sphere.reg surface or the -contrsurfreg option for that matter, but if it is what I surmise it to be we should be able to run MapIcosahedron on it and get standard meshes with node numbers that would match those on the contralateral side.
The easiest thing would be if you could send me the whole FreeSurfer output for one subject that you processed with the -contrsurfreg option and I can adapt the script to deal with such surfaces automatically. If you want to go this route, send me an email and I'll send you upload instructions.


As an
> alternative, after generating both lh and rh
> surfaces in SUMA, is there a way to reorder the
> nodes of the right hemisphere to match the anatomy
> of the left hemi?

There is, it is based on the method detailed in the Gotts, Jo, et al. PNAS 2013 (Two distinct forms of functional lateralization in the human brain) paper. There is no command line tool to remesh the surfaces for that purpose however but I can write something to remesh surfaces, and remap datasets, for that purpose.
>
> thanks in advance,
> ~michael
cheers,
Ziad