Re: [Freesurfer] re Annotation2label
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 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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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. > > ___ 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.
Re: [Freesurfer] re Annotation2label
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 gr...@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.
[Freesurfer] re Annotation2label
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 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.
