There is already a label called ?h.cortex.label for all of cortex. For lobes, you can use mris_annotation2label to break up the annotation into its constituent labels, then use mri_mergelabels to combine subsets into a lobe, then use mris_label2annot to combine the lobes into a new annotation. Search through the mail archives because this has been asked/answered before
On 08/21/2016 01:43 PM, Adil Javed wrote: > Thanks, > > any thoughts about Q#2: > 2-Also, Is there a way to segment the cortices as a whole, like left > and right frontal cx, parietal cx, temporal cx, occipital cx? > > Thanks > > aj > > > On Saturday, August 20, 2016 9:21 PM, "sha...@nmr.mgh.harvard.edu" > <sha...@nmr.mgh.harvard.edu> wrote: > > > Hi Adil, > My understanding is that, you can always change the location of > SUBJECTS_DIR. Just use this command: > setenv SUBJECTS_DIR <Your location of interest> > > You do not need to mention this new address in your recon-all command. > > Good luck > > > > > HI,1-I'm working with FreeSurfer that is on a server. I don't have > > permission to create files under the $SUBJECTS_DIR. Is there any > way I > > > can specify -subject to be in a directory for which I do have > permission? > > for example: recon-all -subject /location of the file or my own > > subject_dir location -all > > 2-Also, Is there a way to segment the cortices as a whole, like left and > > right frontal cx, parietal cx, temporal cx, occipital cx? > > > > > > Thanks, > > AJ_______________________________________________ > > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > 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 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
