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 > <[email protected] <mailto:[email protected]>> 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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > <mailto:[email protected]> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] <mailto:[email protected]> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > [email protected] <mailto:[email protected]> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
