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

Not sure if I followed. Does the look up table have the labels at all? > On May 15, 2017, at 7:46 PM, Bruce Fischl wrote: > > hmm, not sure. Ruopeng? > > On Mon, 15 May 2017, Lukas Pezenka wrote: > >> Thank you. The tip about Christophe's parcellation was very

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

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"

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

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

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

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

You need to use a valid output format like mgh, mgz, nii, etc (eg, surf/lh.inflated.mgh). Also, you should not run vol2surf mapping to the inflated surface as this surface is mostly outside the head. Use the default white surface and then visualize on the inflated only On 05/12/2017 10:18 AM,

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 > >

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

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

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.