hmm, not sure. Ruopeng? On Mon, 15 May 2017, Lukas Pezenka wrote:
> Thank you. The tip about Christophe's parcellation was very helpful - I > can actually see the sulcal labels in freesurfer when loading > aparc.a2009s+aparc volume. Oddly enough, when I check the "show existing > labels only" box, none of them is displayed - I wonder why that is? > > I should, in any case, be able to build the map now. Thank you! > > Best regards, > > Lukas > > On 15.05.2017 18:38, Bruce Fischl wrote: >> no, they shouldn't be labeled as 0. You can create your own though, >> possibly using Christophe's parcellation instead of the aparc.annot >> (check in recon-all.cmd to see how to run it). Christophe's has sulci >> labeled separately so might be better for your purposes. Or you could >> create your own from your own label(s) >> On Mon, 15 May 2017, Lukas Pezenka >> wrote: >> >>> Hi Bruce, >>> >>> not sure - from what I see, sulci are labelled as 0 in the wmparc, are >>> they not? In my understanding, only gyri are actually labelled... I >>> might as well get that totally wrong, though, so sorry if I do... >>> >>> Best regards, >>> >>> Lukas >>> >>> >>> On 15.05.2017 15:53, Bruce Fischl wrote: >>>> Hi Lukas >>>> >>>> lh.sulc is not a surface - it's a scalar field over the surface. Have you >>>> looked at the wmparc? Does it not fill your needs? >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 15 >>>> May 2017, Lukas Pezenka wrote: >>>> >>>>> Hi all, >>>>> >>>>> here's my follow-up: I've now tried to use mris_fill on my lh.sulc. >>>>> However, I got the error message that "there are many more faces than >>>>> vertices". Running recon-all on this dataset takes 30+ hours on my >>>>> machine, hence I don't want to do it again unless it is absolutely >>>>> necessary. >>>>> >>>>> Can anybody recommend another way (or a solution to either my >>>>> mri_surf2vol or mris_fill problems) of obtaining a binary sulcus mask? >>>>> I'm in desperate need of one.. >>>>> >>>>> Best regards, >>>>> >>>>> Lukas >>>>> >>>>> >>>>> On 12.05.2017 16:18, Lukas Pezenka wrote: >>>>>> Hi all, >>>>>> >>>>>> I need a volume that maps my sulci. So first I've run recon-all on my >>>>>> data. Worked like a charm. Visual verification in freeview shows that >>>>>> the inflated surface looks just about right (although it does not seem >>>>>> to be registered to the aparc+aseg volume). However, when I try to run >>>>>> mri_surf2vol, I get the error message "ERROR: cannot recognize the type >>>>>> of surf/lh.inflated". >>>>>> >>>>>> My precise syntax was mri_surf2vol --o out.nii --identity casestudy2 >>>>>> --surf inflated --hemi --lh --surfval surf/lh.inflated >>>>>> >>>>>> Can anyone advise me on this? >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Lukas >>>>>> >>>>>> PS :I'm running on FS version 5.3.0. >>>>>> PPS: Is it possible to achieve this from freeview rather than from the >>>>>> command line? >>>>>> _______________________________________________ >>>>>> 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 >>> >>> >>> >> _______________________________________________ >> 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
