[Simnibs-discuss] E-field brain matter options

Tue Mar 7 19:37:27 CET 2023

Ok, I will try that. Thank you so much for your help!!

Summer

From: Oula Puonti <oulap at drcmr.dk>
Date: Friday, March 3, 2023 at 1:19 PM
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,

Aah, I see. Yeah at the moment there is no option to specify the
tissues in the GUI. If you want to hardcode this for your specific
simnibs version you should edit line 193 inside the sim_struct.py file.
You can find the file inside

<simnibs_installation_path>/simnibs/simulation

and you should change the default tissues used, see

https://secure-web.cisco.com/1LCPc7FEkoNfGimTxGj3_92cFiJfmIX7GDeoqM2rTORaTLrOLIFFfBEBf8C7AeKguZP_-L6TapgGGd1brWzOnpX16McHb0Ka6x-XyEeGqynQ22d9uDyK5z1-KAs2ZwUpDJML1fcRmc-pXHlwhnZEnM_PncuRRW-xUrVAhxk8AuVgxZSr6iIqtGq3X47g5PXPQt6PgzcP86StGVIVsOMfbLfOxp6DiWMs7VIDzbrY5EtaNGEKzgvq9EwR5BPnHiGUIYjgijQoO4oih_Wlu4igl0yUSuhxKH8YAUsKRic9ybucIyl1VwDvTC9reXc6VfmNz/https%3A%2F%2Fgithub.com%2Fsimnibs%2Fsimnibs%2Fblob%2Fmaster%2Fsimnibs%2Fsimulation%2Fsim_struct.py%23L193

Best,
Oula

On Fri, 2023-03-03 at 15:18 +0000, Frandsen, Summer Brianne wrote:
> 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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