Re: [Freesurfer] using custom surface template

sounds good. Bruce

On Thu, 20 Dec 2018, Jason Tourville wrote:

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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 fischl@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
  >
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-- 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