I guess you could use the ribbon.mgz and mask it with various labels in the aparc+aseg.mgz
cheers Bruce On Wed, 29 Dec 2010, FIDEL ALFARO ALMAGRO wrote: > Hello experts, > > After several days of trying, I have accomplished to get what you thought > I was asking for. Unfortunately I was not asking for that. > > First, I have to say that there is no --lobes option in > mri_annotation2label (It is not documented, and if you try it, nothing > happens). > > Then I ran these commands: > > [1] mri_annotation2label --subject XXX --hemi rh --outdir > ../subjects/XXX/tmp/ --annotation lobes > > [2] mri_label2vol --label ../subjects/XXX/rh.temporal.label --subject XXX > --o test.nii --temp ../subjects/XXX/mri/orig.mgz --identity > > I have seen that what I get in test.nii is a volume with the segmentation > of the border between the white matter and grey matter in the temporal > lobe. I am afraid I was not clear enough, as I was looking for a volume > with the segmentation of the grey matter of the temporal lobe. I have > tried changing the parameters in the first command, but it does not seem > to work. > > Does anybody know how can I do this? > > Thanks in advance. > > Fidel. > > >> Thank you very much for the quick answer and happy holidays. >> >>> Forwarding a previous answer from doug. I tried it before (and >>> recently). It does seem to work. >>> >>>>>> >>>>>> Try running mri_annotation2label with --lobes lh.lobes.annot >>>>>> >>>>>> doug >>>>>> >>>>>> >>>>>> On Thu, 20 May 2010, Rudolph Pienaar wrote: >>>>>> >>>>>>> Hi all -- >>>>>>> >>>>>>> Is there a simple way to create an annotation for >>>>>>> frontal/temporal/occipital/parietal lobes based off the ? >>>>>>> h.aparc.annot >>>>>>> files in a FS 'label' dir? Ideally speaking, I'd like to have a >>>>>>> ?h.lobar.annot with corresponding lobar.annot.ctab. >>>>>>> >>>>>>> Apologies if this question has come up before... a quick google >>>>>>> didn't >>>>>>> reveal anything. >>>>>>> >>>>>>> Many thanks >>>>>>> -=R >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >>> On Dec 24, 2010, at 10:39 AM, FIDEL ALFARO ALMAGRO wrote: >>> >>>> Hello, >>>> >>>> I am trying to obtain a segmentation of the cortex to get the >>>> different >>>> lobes (specifically, the temporal lobe). I have read (via google) that >>>> someone asked that before in this mailing list, but the answer was >>>> old and >>>> not very clear, so I guessed this program was the solution. >>>> >>>> So... Is there any tool in the freesurfer suite to allow me to get a >>>> segmentation of the different lobes of the brain? >>>> >>>> Thanks. >>>> >>>>> Hi Fidel, >>>>> >>>>> that is deprecated code. What are you trying to do? >>>>> >>>>> cheers (and happy holidays) >>>>> >>>>> Bruce >>>>> On Fri, 24 Dec 2010, >>>>> FIDEL ALFARO ALMAGRO wrote: >>>>> >>>>>> Happy holidays for those who celebrate it today, >>>>>> >>>>>> Hi. Is there any documentation on how to use mri_mark_temporal_lobe >>>>>> application and what is its output? I cannot find any. >>>>>> >>>>>> Thanks in advance. >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>> >>> >> >> >> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
