Hi Jason

we use the parcellation to figure out where we don't need to deform the
pial surface. I expect our standard parcellation is good enough for this,
so maybe you can just run your own posthoc?

cheers
Bruce


On Wed, 19 Dec 2018, Jason Tourville wrote:

>
>         External Email - Use Caution        
>
> Hello FreeSurfers,We use a custom surface template, generated according to the instructions in the
> SurfaceRegAndTemplates instructions for inter-subject co-registration. We then do cortical labeling
> and extract surface and volume stats. In the past, I would re-run mris_register, then jump to
> labeling using the resulting ?h.sphere.reg (using either a custom atlas or the labeled template
> surface), and then extract stats. However, I now see that there are steps in -autorecon3 stage of
> the recon-all workflow, including the pial surface generation step, that are done after the -surfreg
> step, but prior to stat extraction, that depend on ?h.sphere.reg. So it seems like I should be
> running the essentially the entire -autorecon3 stage (minus -sphere and the default surface labeling
> and stat extraction steps) with the custom surface template as input. Is that the case? If so, is
> there an "expert flag" to run these steps of -autorecon3 with a custom surface template (analogous
> to the -custom-tal-atlas flag for early stages?)
>
> Thanks,
> Jason 
>
> --
> Jason A. Tourville, Ph.D.
> Research Assistant Professor
> Department of Speech, Language,
> and Hearing Sciences
> Boston University
> 677 Beacon St.
> Boston, MA 02215
> Phone: (617)353-9484
> Fax: (617)353-7755
>
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