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
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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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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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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> 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 Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
What about volume? For surface, it seems that it is ok. On Tue, Aug 22, 2017 at 1:29 AM Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> 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 Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Fereshte