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 gr...@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 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.
[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.
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.
