Hello Freesurfers,
I would like to be able to display just a few parcels from the Desikan atlas on the fsaverage inflated surface. For example, I would like to display only the superiorfrontal and the posteriorcingulate. I tried to recreate the parcels myself by drawing labels, but they don't look pretty (see the attachment). I traced the labels in qdec (based on the Annotation/Opacity tab) and then I mapped them to fsaverage and visualized them with freeview.
There's probably a better way to do that but I couldn't figure it out. Can anyone help me with this?
Thanks! Mihaela
Break up the annot into separate labels then recombine the ones you want into a new annotation. Use mri_annotation2label for the first step then mris_label2annot for the second.
On 10/27/2015 02:35 PM, Mihaela Stefan wrote:
Hello Freesurfers,
I would like to be able to display just a few parcels from the Desikan atlas on the fsaverage inflated surface. For example, I would like to display only the superiorfrontal and the posteriorcingulate. I tried to recreate the parcels myself by drawing labels, but they don't look pretty (see the attachment). I traced the labels in qdec (based on the Annotation/Opacity tab) and then I mapped them to fsaverage and visualized them with freeview.
There's probably a better way to do that but I couldn't figure it out. Can anyone help me with this?
Thanks! Mihaela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks! Mihaela
On Wed, Oct 28, 2015 at 1:29 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Break up the annot into separate labels then recombine the ones you want into a new annotation. Use mri_annotation2label for the first step then mris_label2annot for the second.
On 10/27/2015 02:35 PM, Mihaela Stefan wrote:
Hello Freesurfers,
I would like to be able to display just a few parcels from the Desikan atlas on the fsaverage inflated surface. For example, I would like to display only the superiorfrontal and the posteriorcingulate. I tried to recreate the parcels myself by drawing labels, but they don't look pretty (see the attachment). I traced the labels in qdec (based on the Annotation/Opacity tab) and then I mapped them to fsaverage and visualized them with freeview.
There's probably a better way to do that but I couldn't figure it out. Can anyone help me with this?
Thanks! Mihaela
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
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.
Hi Doug,
I am going back to this old email. I was able to brake the annot file into separate labels and I created a new annotation file with only the labels that I was interested in. However, the inflated surface disappears when I upload my own annotation in freeview. Only the labels are shown (see attachment). If I select "show outline only", then the inflated surface remains displayed. How can I keep the inflated surface displayed while I am loading the annotation file?
On a different note, I could upload multiple labels in the same time in freeview in the past. Now I can only upload one label at the time. I wonder if there is some setting that I am missing.
Thanks! Mihaela
On Wed, Oct 28, 2015 at 1:29 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Break up the annot into separate labels then recombine the ones you want into a new annotation. Use mri_annotation2label for the first step then mris_label2annot for the second.
On 10/27/2015 02:35 PM, Mihaela Stefan wrote:
Hello Freesurfers,
I would like to be able to display just a few parcels from the Desikan atlas on the fsaverage inflated surface. For example, I would like to display only the superiorfrontal and the posteriorcingulate. I tried to recreate the parcels myself by drawing labels, but they don't look pretty (see the attachment). I traced the labels in qdec (based on the Annotation/Opacity tab) and then I mapped them to fsaverage and visualized them with freeview.
There's probably a better way to do that but I couldn't figure it out. Can anyone help me with this?
Thanks! Mihaela
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
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.
How does it look in tksurfer?
On 01/04/2016 03:29 PM, Mihaela Stefan wrote:
Hi Doug,
I am going back to this old email. I was able to brake the annot file into separate labels and I created a new annotation file with only the labels that I was interested in. However, the inflated surface disappears when I upload my own annotation in freeview. Only the labels are shown (see attachment). If I select "show outline only", then the inflated surface remains displayed. How can I keep the inflated surface displayed while I am loading the annotation file?
On a different note, I could upload multiple labels in the same time in freeview in the past. Now I can only upload one label at the time. I wonder if there is some setting that I am missing.
Thanks! Mihaela
On Wed, Oct 28, 2015 at 1:29 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Break up the annot into separate labels then recombine the ones you want into a new annotation. Use mri_annotation2label for the first step then mris_label2annot for the second. On 10/27/2015 02:35 PM, Mihaela Stefan wrote: > Hello Freesurfers, > > I would like to be able to display just a few parcels from the Desikan > atlas on the fsaverage inflated surface. For example, I would like to > display only the superiorfrontal and the posteriorcingulate. I tried > to recreate the parcels myself by drawing labels, but they don't look > pretty (see the attachment). > I traced the labels in qdec (based on the Annotation/Opacity tab) and > then I mapped them to fsaverage and visualized them with freeview. > > There's probably a better way to do that but I couldn't figure it out. > Can anyone help me with this? > > Thanks! > Mihaela > > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel: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
It worked in tksurfer! Thanks! Mihaela
On Tue, Jan 5, 2016 at 1:13 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
How does it look in tksurfer?
On 01/04/2016 03:29 PM, Mihaela Stefan wrote:
Hi Doug,
I am going back to this old email. I was able to brake the annot file into separate labels and I created a new annotation file with only the labels that I was interested in. However, the inflated surface disappears when I upload my own annotation in freeview. Only the labels are shown (see attachment). If I select "show outline only", then the inflated surface remains displayed. How can I keep the inflated surface displayed while I am loading the annotation file?
On a different note, I could upload multiple labels in the same time in freeview in the past. Now I can only upload one label at the time. I wonder if there is some setting that I am missing.
Thanks! Mihaela
On Wed, Oct 28, 2015 at 1:29 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Break up the annot into separate labels then recombine the ones you want into a new annotation. Use mri_annotation2label for the first step then mris_label2annot for the second. On 10/27/2015 02:35 PM, Mihaela Stefan wrote: > Hello Freesurfers, > > I would like to be able to display just a few parcels from the Desikan > atlas on the fsaverage inflated surface. For example, I would like to > display only the superiorfrontal and the posteriorcingulate. Itried
> to recreate the parcels myself by drawing labels, but they don't look > pretty (see the attachment). > I traced the labels in qdec (based on the Annotation/Opacity tab) and > then I mapped them to fsaverage and visualized them with freeview. > > There's probably a better way to do that but I couldn't figure it out. > Can anyone help me with this? > > Thanks! > Mihaela > > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel: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
ok, that means a bug in freeview.
On 01/05/2016 02:15 PM, Mihaela Stefan wrote:
It worked in tksurfer! Thanks! Mihaela
On Tue, Jan 5, 2016 at 1:13 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
How does it look in tksurfer? On 01/04/2016 03:29 PM, Mihaela Stefan wrote: > Hi Doug, > > I am going back to this old email. > I was able to brake the annot file into separate labels and I created > a new annotation file with only the labels that I was interested in. > However, the inflated surface disappears when I upload my own > annotation in freeview. Only the labels are shown (see attachment). If > I select "show outline only", then the inflated surface remains > displayed. How can I keep the inflated surface displayed while I am > loading the annotation file? > > On a different note, I could upload multiple labels in the same time > in freeview in the past. Now I can only upload one label at the time. > I wonder if there is some setting that I am missing. > > Thanks! > Mihaela > > On Wed, Oct 28, 2015 at 1:29 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > Break up the annot into separate labels then recombine the ones > you want > into a new annotation. Use mri_annotation2label for the first step > then > mris_label2annot for the second. > > > On 10/27/2015 02:35 PM, Mihaela Stefan wrote: > > Hello Freesurfers, > > > > I would like to be able to display just a few parcels from the > Desikan > > atlas on the fsaverage inflated surface. For example, I would > like to > > display only the superiorfrontal and the posteriorcingulate. I tried > > to recreate the parcels myself by drawing labels, but they don't > look > > pretty (see the attachment). > > I traced the labels in qdec (based on the Annotation/Opacity > tab) and > > then I mapped them to fsaverage and visualized them with freeview. > > > > There's probably a better way to do that but I couldn't figure > it out. > > Can anyone help me with this? > > > > Thanks! > > Mihaela > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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> <mailto: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 <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 <tel:617-724-2358> Fax: 617-726-7422 <tel: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
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freesurfer@nmr.mgh.harvard.edu
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Mihaela Stefan