External Email - Use Caution Hi Doug, I'm using this command: mri_label2label --srclabel lh.fusiform.label --trglabel output.label --s sub01 --regmethod surface --hemi lh --outmask outmask.gii Best regards, Sam
On Fri, Jul 10, 2020 at 9:48 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > what's your mri_label2label command? > > On 7/10/2020 3:05 PM, Sam W wrote: > > External Email - Use Caution > Hi Doug and Tim, > I'm running probtrackx with freesurfer surfaces as seeds. However > probtrackx requires a file that contains both the whole surface file (eg, > lh.pial) as well as the overlay (the scalar values associated with the > vertices of the roi). > I can create such a file with FSL's label2surf command which creates a > gifti file that encodes both the surface and the overlay. > My question is whether I can do the same with freesurfer? Running > probtrackx with the overlay from mri_label2label --outmask does not work. > It also needs the associated pial or white surface. > Best regards, > Sam > > > On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> what do you mean merge with the pial? >> >> On 7/9/2020 8:07 PM, Sam W wrote: >> >> External Email - Use Caution >> It works great Doug, thanks a lot! >> Can I ask you a follow up question please? I created the overlay with >> mri_label2label using --outmask as you suggested, but now I'd like to merge >> that overlay with the pial surface (lh.pial). Is there a tool I can use to >> achieve that result? >> Best regards, >> Sam >> >> >> On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve <dgr...@mgh.harvard.edu> >> wrote: >> >>> Use mri_label2label with the --outmask option >>> >>> On 7/8/2020 10:14 PM, Sam W wrote: >>> >>> External Email - Use Caution >>> Hi, >>> Is there a way to convert a label file into a surface/overlay? Thank you! >>> Best regards, >>> Sam >>> >>> _______________________________________________ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://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 >> listfreesur...@nmr.mgh.harvard.eduhttps://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 > listfreesur...@nmr.mgh.harvard.eduhttps://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
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