[Simnibs-discuss] Normal component E-field in Matlab after optimization

[Beumer, Steven]

Dear Fang and the SimNibs team,
.
Thank you for your answer, I understand the error in my reasoning indeed with map_to_surf, I use Matlab for my development and I would like to have my mesh in FsAverage indeed. The problem that I have though is that I would like to have this after an optimization call, which also returns the fields, instead of after a tDCS simulation. 

Using the following does not yield the mapped fields (probably because opt_struct doesn't have those options) :
S = opt_struct('TDCSoptimize');
S.map_to_fsavg = true;
S.map_to_mni = true;

A workaround would be to simulate the optimized structure with the flags put to true, however I was curious if there would be a more elegant solution to this. 
Is there a solution for this or should I go for the workaround?

Kind regards and many thanks for your help,
Steven

-----Original Message-----
From: fangc <fangc at drcmr.dk> 
Sent: Wednesday, June 9, 2021 10:57 AM
To: Beumer, Steven <s.beumer at tue.nl>
Cc: simnibs-discuss at drcmr.dk
Subject: Re: [Simnibs-discuss] Normal component E-field in Matlab after optimization

Dear Steven,

The attribute 'map_to_surf' will map your results to the gray matter central surface and not give you the normal component of the E field. 
What you want to do might be a little post-processing. I do not know which language you use for your development, but in python you can simply do the following, for example, if you have a mesh in FsAverage
space:

field_name = 'E_normal'
results_fsavg.field[field_name].value

You can find more details here:
https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsimnibs.github.io%2Fsimnibs%2Fbuild%2Fhtml%2Ftutorial%2Fadvanced%2Fgroup_analysis.html%3Fhighlight%3Dnormal&data=04%7C01%7C%7Cd72f4185a1954759b71208d92b2488d8%7Ccc7df24760ce4a0f9d75704cf60efc64%7C1%7C1%7C637588258179721089%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=eYAXvGd%2FbxSvJnXoIoBUbF6IHgv1fVQR%2FmBiY9HoQDk%3D&reserved=0

It also has a Matlab example for the same purpose. Good luck. And please let us know if you have further questions.

Best,
Fang

On 2021-06-08 12:38, Beumer, Steven wrote:
> Dear SimNibs team,
> 
> I am writing a little MATLAB app to do optimizations in SimNibs via a 
> GUI, which is going very well.
> 
> In the GUI I would like to plot the fields and the histogram, which I 
> do via the standard data reading scripts, however I have troubles 
> getting the normal component of the E-field.
> 
> I tried giving the optimization structure a map_to_surf = true 
> attribute, which does not work. Is there a way to get the normal 
> component without doing the simulation afterwards with the optimized 
> electrodes?
> 
> Kind regards and a lot of thanks in advance,
> 
> Steven Beumer
> 
> PhD student at the Eindhoven University of Technology 
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