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Hello Ryan,
On June 26, 2019 at 9:26 PM "Nillo, Ryan Michael R" RyanMichael.Nillo@ucsf.edu wrote: [...] I want to generate a smooth pial surface similar to the one displayed on the LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI https://surfer.nmr.mgh.harvard.edu/fswiki/LGI) without having to run the entire recon-all process.
I'm not 100% sure what you want as the output, but if it is a surface file (like ?h.white or pial) I think the easiest way is to follow the commands listed on the LGI wiki page you linked, under the section "Processing Stream" up to the point that you need. Most likely you can stop after step 4, when ?h.pial-outer-smoothed has been produced.
Additionally, I want to map this surface to the white surface. Is there an easy way to do this?
I am not sure what you mean by this. Could you explain what would be the inputs and the expected output files of this process?
If you mean that the vertex indices in the meshes of the white and your pial-outer-smoothed surface files should match: this should be the case by default I guess.
Best,
Tim
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany