[Simnibs-discuss] E-field brain matter options

[Frandsen, Summer Brianne]

Hi Oula.

Sorry, I should have clarified! I’m talking about the nifti files that are output when using the simnibs simulation GUI. The only files I can get output are the ones with gray matter tissue.

Thanks,

Summer

From: Oula Puonti <oulap at drcmr.dk>
Date: Friday, March 3, 2023 at 8:33 AM
To: Frandsen, Summer Brianne <sfrandsen at bwh.harvard.edu>, discuss at simnibs.org <discuss at simnibs.org>
Subject: Re: [Simnibs-discuss] E-field brain matter options
        External Email - Use Caution

Hi Summer,

Just to make sure: are we talking about gmsh or the simnibs simulation
GUI?

The simulated electric field is always calculated in all tissues so you
can visualize the field in both the gray and white matter in gmsh. The
surfaces and volumes between v4 and v3 look a bit different now, for
example the spinal cord is now fully white matter without a gray matter
layer around it.

In the simulation GUI the only brain surface you can visualize is the
gray matter surface.

Best,
Oula


On Thu, 2023-03-02 at 20:34 +0000, Frandsen, Summer Brianne wrote:
> Hi,
>
> In previous SimNIBS versions (e.g. V 3.2.6), the default electric
> field modeling simulations included both grey and white matter when
> using the gui. However, the newest version appears to be use only
> grey matter. It seems like there is a way to change this option (e.g.
> including white matter) when scripting simulations, but I have been
> unable to find an option that allows me to do in the gui. Is there a
> way to do this in the gui?
>
> Thanks,
>
> Summer. Frandsen
>
>
>
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