[Simnibs-discuss] Use head mesh obtained from FreeSurfer

Axel Thielscher axelt at drcmr.dk
Tue Oct 11 13:11:04 CEST 2022

Hi Silvana,

I haven't worked with TVB on my own. From an earlier request, it seems 
that TVB also has tissue masks as nifti-volumes. Then you don't need 
surfaces to create a head model.

You just have to create one nifti file where the compartment labels 
follow the simnibs conventions: 1 WM, 2 GM, 3 CSF, 4 SKULL, 5 SKIN. If 
you would like to distinguish between more comparments, let me know.

The run the /meshmesh /command of simnibs4 
(https://github.com/simnibs/simnibs/releases/tag/v4.0-beta1) to get a 
volume mesh for field simulations.

Hope this helps.

Best regards,


On 27-09-2022 16:27, Huertas Penen, Silvana (UT-EEMCS) wrote:
> Hi everyone,
> I’m working with The virtual brain (TVB) and SimNibs, and I need to be 
> able to use the head mesh from TVB in SimNIBS.
> The head mesh from TVB is calculated using FreeSufer. Do you have any 
> clue if I can use the mesh obtained from Freesurfer in SimNIBS?
> The FreeSurfer gives me the mesh in zip files, having face and vertex 
> information.
> Kind regards,
> Silvana
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

Dr. Axel Thielscher
Professor of Neurophysics and Neuroimaging
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
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