[pymvpa] pial and white surfaces for surface-based searchlight?

Nick Oosterhof n.n.oosterhof at googlemail.com
Sun Jan 31 17:02:51 UTC 2016

> On 30 Jan 2016, at 17:09, Maria Hakonen <maria.hakonen at gmail.com> wrote:
> I would like to try surface-based searchlight. I have now reconstructed the inner (white) and outer (pial) surfaces using FreeSurfer autorecon-all. Is there any way to check if the surfaces are successfully reconstructed? 

The pymvpa2-prep-afni-surf script can be used for surface preprocessing. It requires working FreeSurfer, PyMVPA and AFNI packages. Run "suma -spec your_spec_file.spec" to visualize the surfaces in SUMA. 

It can be used to align surfaces to either an anatomical or functional volume. It can also resample surfaces to standard topology and merges left and right hemispheres. Recent versions of the script generate some QA images that may be useful to verify coregistration. But in the end, it's usually best to view surfaces together with an anatomical overlay to check whether the surfaces are properly reconstructed and aligned. 

Does that answer your question?

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