Hi all,
I bit confused about how to create labels from annotation2label command to create DLPFC. I want make DLPFC label by merging G_frontal_middle.label, S_frontal_inferior.label and S_frontal_middle.label (available in the 2009 atlas). But I only can get annotation2label to work with the other atlas; eg using this command:
mri_annotation2label --subject $subject --hemi rh --outdir ./$subject/label
But I would like 2009 atlas so for example
mri_annotation2label --a2009s --subject $subject --hemi rh --outdir ./subject/label
But this flag doesnt seem to work. Any other suggestions to get the label files (so i can then do mri_mergelabels and Mris_anatomical stats would be very appreciated, I dont think I need use tksurfer, I think mri_annotation2label should work somehow?
Kind Wishes,
Linn
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*
Use --annotation aparc.a2009s Run it with --help to see all the options. doug
On 08/06/2013 08:24 AM, Linn Mittlestein wrote:
Hi all,
I bit confused about how to create labels from annotation2label command to create DLPFC. I want make DLPFC label by merging G_frontal_middle.label, S_frontal_inferior.label and S_frontal_middle.label (available in the 2009 atlas). But I only can get annotation2label to work with the other atlas; eg using this command:
mri_annotation2label --subject $subject --hemi rh --outdir ./$subject/label
But I would like 2009 atlas so for example
mri_annotation2label --a2009s --subject $subject --hemi rh --outdir ./subject/label
But this flag doesnt seem to work. Any other suggestions to get the label files (so i can then do mri_mergelabels and Mris_anatomical stats would be very appreciated, I dont think I need use tksurfer, I think mri_annotation2label should work somehow?
Kind Wishes,
Linn
/
/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you. I also have one question; it says default is "white" surface, but I want measure cortical thickness. Can I leave white in or do I change --surf to gray for this?
Kind Wishes,
Linn
On Tue, Aug 6, 2013 at 6:50 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Use --annotation aparc.a2009s Run it with --help to see all the options. doug
On 08/06/2013 08:24 AM, Linn Mittlestein wrote:
Hi all,
I bit confused about how to create labels from annotation2label command to create DLPFC. I want make DLPFC label by merging G_frontal_middle.label, S_frontal_inferior.label and S_frontal_middle.label (available in the 2009 atlas). But I only can get annotation2label to work with the other atlas; eg using this command:
mri_annotation2label --subject $subject --hemi rh --outdir ./$subject/label
But I would like 2009 atlas so for example
mri_annotation2label --a2009s --subject $subject --hemi rh --outdir ./subject/label
But this flag doesnt seem to work. Any other suggestions to get the label files (so i can then do mri_mergelabels and Mris_anatomical stats would be very appreciated, I dont think I need use tksurfer, I think mri_annotation2label should work somehow?
Kind Wishes,
Linn
/
/
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 Linn, just leave it as white. The label is just a list of vertices. doug
On 08/07/2013 05:38 AM, Linn Mittlestein wrote:
Thank you. I also have one question; it says default is "white" surface, but I want measure cortical thickness. Can I leave white in or do I change --surf to gray for this?
Kind Wishes,
Linn
On Tue, Aug 6, 2013 at 6:50 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Use --annotation aparc.a2009s Run it with --help to see all the options. doug On 08/06/2013 08:24 AM, Linn Mittlestein wrote: > Hi all, > > I bit confused about how to create labels from annotation2label > command to create DLPFC. I want make DLPFC label by merging > G_frontal_middle.label, S_frontal_inferior.label and > S_frontal_middle.label (available in the 2009 atlas). But I only can > get annotation2label to work with the other atlas; eg using this command: > > mri_annotation2label --subject $subject --hemi rh --outdir > ./$subject/label > > But I would like 2009 atlas so for example > > mri_annotation2label --a2009s --subject $subject --hemi rh --outdir > ./subject/label > > But this flag doesnt seem to work. Any other suggestions to get the > label files (so i can then do mri_mergelabels and Mris_anatomical > stats would be very appreciated, I dont think I need use tksurfer, I > think mri_annotation2label should work somehow? > > Kind Wishes, > > Linn > > > / > > / > > > _______________________________________________ > 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@nmr.mgh.harvard.edu
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Linn Mittlestein