[Simnibs-discuss] Working on a "generic" head model

Axel Thielscher axelt at drcmr.dk
Wed Jan 13 14:32:28 CET 2021

Dear Kris,

please see my comments below.



On 1/13/2021 1:21 PM, Kris BAETENS wrote:
> Dear SimNibs users,
> I want to compare several tDCS montages and assess field strength in 
> particular ROI’s, on a “generic” head model, prior to actually 
> starting the study. I thought the MNI152 example mesh could serve 
> perfectly for this purpose. However, I struggle with some very 
> beginner technical issues.
>   * Am I correct in assuming that this mesh is already in MNI space?
>   * “Transform to MNI space” under simulation options fails,
>     supposedly because the m2m folder doesn’t contain the necessary
>     information?
As it is already in MNI space, there is no transformation required. Just 
use "Interpolate to a nifti volume" instead.
>   * Similarly, the mni2subject_coords call in the example ROI script
>     fails, again, I assume again because the m2m folder doesn’t
>     contain the necessary information? (I can get it to run without a
>     problem on Ernie).
This call is not needed. Just use the coordinates without any 
>   * Is it possible to calculate mean field strength in an anatomical
>     (e.g., atlas-based) ROI, rather than using the sphere-based
>     approach? (I wanted to approach this from a “masking” angle, but
>     am unsure how to proceed, as I cannot transform the standard head
>     simulation to MNI space).
Yes. The results which you get when using "Interpolate to a nifti 
volume" are already in MNI space, and you can apply any ROI that is in 
MNI space.

Best regards,


> Thank you very much for making this wonderful software and also making 
> the tutorials publicly available on youtube!
> Kind regards,
> Kris Baetens
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> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

Dr. Axel Thielscher
Associate Professor
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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