Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated
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
Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated
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
Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated
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] mri_surf2vol cannot recognize the type of surf/lh.inflated
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.
