[Simnibs-discuss] Question about BCs and getting nodal potentials

[Axel Thielscher]

Hi Hassan,

please see below.

On 12/21/2021 2:26 PM, Hassan Yazdanian wrote:
>
> Hello,
>
> I am trying y to compare the result obtained by SimNIBS with that one 
> calculated by FEniCS (https://fenicsproject.org/) for a tDCS 
> simulation. For this purpose, I have imported .msh file generated by a 
> SimNIBS simulation into FEniCS. I have used the spherical model 
> provided in SimNIBS dataset. Now, I have two questions:
>
> 1-How can I get the electrical potentials of nodes and corresponding 
> nodal coordinates? In earlier versions of SimNIBS, I used “v = 
> fem.tdcs_getdp”. I was wondering if there is a similar command in 
> SimNIBS 3.2.
>
You can add a 'v' to the 'fields' attribute when defining the simulation:

https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/session.html

The potential will then be added as node_data to the results mesh. The 
nodal positions are stored under the "nodes" parameter:

https://simnibs.github.io/simnibs/build/html/documentation/python_lib/auto/simnibs.Msh.html#simnibs.Msh

> 2-About applying boundary condition, as I understood, SimNIBS uses a 
> constant potential on electrodes (Say -1 on Cathode and 0 on Anode). 
> After solving the FEM system of equations, then potentials are scaled 
> to reach the given current set for electrodes ( I mean we know the 
> potential on 2101 and 1501 surfaces, both side of Anode, and we know 
> the conductivity of the electrode, 29.4 S/m, then we can determine the 
> current passing through the electrode). Am I right?
>
Yes, that's correct.

Merry Christmas and a good start into the new year to you, too!

Best,

Axel


> Merry Christmas and Happy new year in advance!
>
> Best wishes,
>
> -Hassan
>
>
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-- 
Dr. Axel Thielscher
Professor of Neurophysics and Neuroimaging
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
www.drcmr.dk
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/
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