Which version of FS are you using? It should be in version 5 (though it is undocumented). Are you sure it did not create a lobes annotation in the subject's label dir? The reason that it is undocumented is that it does not quite do what people really want (it keeps pre and post central gyrus for example). I would use --lobesStrict instead of --lobes (this is in version 5.1). You can also create your own by merging the aparc labels (mri_mergelabels) and then creating a new annot from the merged labels (mris_label2annot).
doug On 12/29/10 11:38 AM, 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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
