whatever annotation you give it (eg, aparc). There are not separate
labels for the inner and the outer. The distinction is in the xyz
coordinates. If you don't give it a surface, it will use the xyz coords
from the inner (white) surface. If you give it --surface pial, it will
use the xyz coords from the outer



On 08/21/2017 04:33 PM, Fereshte wrote:
> And what labels does this mri_annotation2label give? Does it give the
> outer cortical boundary as well?
> On Tue, Aug 22, 2017 at 12:19 AM Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>     when you run mri_annotation2label you can specify the surface
>     (--surface). By default, it uses white, but you can specify pial
>     instead
>
>
>     On 08/21/2017 11:33 AM, Fereshte wrote:
>     > Hello FreeSurfer developers,
>     > Is it possible to have the segmentation labels after the pial
>     surface
>     > is done in FreeSurfer? I mean once you do the topology
>     correction and
>     > expand the inner cortical boundary to make the pial surface ; is it
>     > possible to have the inner and outer cortical boundaries as labels
>     > from pial surface?
>     > Looking forward to hearing from you
>     > Sincerely,
>     > Fereshte Ramezani
>     >
>     >
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>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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