External Email - Use Caution Thanks Bruce. I was considering playing around with doing it both ways...seeing if the parcellation based on our template makes a difference, but sounds like it would be small. If I do and find any appreciable difference, will let you know.
Always appreciate the speedy replies. Best, Jason On Wed, Dec 19, 2018 at 2:49 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > 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 > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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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