Thanks for posting back on this. I have tried mri_cor2label and have been unable to understand the --labelid id switch. The documentation and experimentation with it shows that it runs from 0-255 only so this labelid is not the one in FreesurferColorLut.txt . Can you clarify this please.
Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text ________________________________________ From: [email protected] [[email protected]] on behalf of Douglas N Greve [[email protected]] Sent: Tuesday, August 05, 2014 6:04 PM To: [email protected] Subject: Re: [Freesurfer] .label files for subcortical structures You can use mri_cor2label. The output coordinates will be "tkregister-style" RAS, which is probably not useful to you. Check out https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems For how to convert to other coordinate systems doug On 08/05/2014 11:30 AM, Krieger, Donald N. wrote: > > Hi Everyone, > > What tool(s) are used to extract the vectors for subcortical labels? > > What I need are the RAS coordinates for the cerebellum, basal ganglia, > etc. > > Is there something for extracting them from aseg.mgz ? > > Or is there something for generating a .annot file so that > mri_annotation2label may be used? > > Or is there some other way? > > Thanks. > > Don > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
