Re: [Freesurfer] Labels from Pial surface

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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