[Simnibs-discuss] tDCS electrode is being simulated as skin

[Gülce Lale]

Dear Oula,

Thank you for the help. We were able to label electrode gel as background in the segmentation. However, when deriving our electrode center coordinates, we still define the top of the electrode gel. We know that we apply 2mm of electrode gel on top of the electrodes. Thus, the coordinates acquired from the MRI image should be 2mm below, so that they are at the actual skull height. 

How do we convert length measures such as 2mm into world coordinates which SimNIBS uses? And, can I find information on this on the website?

Thank you for your time.
Best wishes,
Gülce

> On 20 Jan 2023, at 19:11, Oula Puonti <oulap at drcmr.dk> wrote:
> 
> Hi Gülce,
> 
> You should leave them out, i.e., label them as background. SimNIBS
> places the electrodes automatically during the simulation, so you don't
> need to add them to the headmodel yourself.
> 
> You can record the center coordinate of the electrodes from the MRI
> scans and pass that to the simulation so that the electrodes are placed
> correctly.
> 
> Best,
> Oula
> 
> 
> On Fri, 2023-01-20 at 17:25 +0100, Gülce Lale wrote:
>> Hi Oula,
>> 
>> Thank you very much for your response, I will try it with charm and
>> SimNIBS4.
>> I would like to clarify something and ask for your opinion. What
>> tissue the electrodes should be segmented as? Should they be left out
>> of the segmentation? Or be segmented as one of the other 15 tissues?
>> 
>> Thank you for your help in advance.
>> Best wishes,
>> Gülce
>> 
>>> On 17 Jan 2023, at 19:54, Oula Puonti <oulap at drcmr.dk> wrote:
>>> 
>>> Hi Gülce,
>>> 
>>> I would consider this a segmentation error. You might want to try
>>> the
>>> new segmentation method (charm) included in simnibs version 4. In
>>> my
>>> experience it does a bit better job on ignoring the electrodes in
>>> the
>>> type of MRI data you have.
>>> 
>>> The other option is that you edit the skin masks, which are inside
>>> the
>>> MASK_prep folder, manually and then re-run the surface and volume
>>> masking steps.
>>> 
>>> The manual editing process was made easier in the new version, see
>>> here: 
>>> 
>>> https://simnibs.github.io/simnibs/build/html/tutorial/advanced/fix_headmodel.html
>>> 
>>> so you might want to consider using SimNIBS4 in any case.
>>> 
>>> Best,
>>> Oula
>>> 
>>> 
>>> On Tue, 2023-01-17 at 15:50 +0100, Gülce Lale wrote:
>>>> Dear SimNIBS Team,
>>>> We conduct post-hoc modelling for each subject using T1 and T2
>>>> images
>>>> acquired while the participant was in the scanner with the tDCS
>>>> electrodes attached. Here SimNIBS headreco images the 2mm layer
>>>> of
>>>> electrode paste and includes in in the head mesh but segments it
>>>> as
>>>> skin (see attached images).
>>>> According to SimNIBS skin conductance is 0.465 s/m and the
>>>> electrode
>>>> material conductivity is 29.4 s/m. One would expect the Ten20
>>>> Electrode paste which is applied with a 2mm thickness between the
>>>> electrode and skin to have a different measure. However, since it
>>>> is
>>>> being considered and modelled as skin this could results in
>>>> deviations in the electric field modelling.
>>>> How do we account/solve this?
>>>> Could we model the electrodes 2mm below the head surface, knowing
>>>> that the outer 2mm thickness of the skin are actually due to the
>>>> paste? Thus, modelling the electrodes on the “actual” skin outer
>>>> layer (and not on top of the paste). SimNIBS then allows us to
>>>> specify past + electrode thickness. Where we assume SimNIBS
>>>> calculates a different conductivity measure for both.
>>>> Is there an alternative solution to best account for the change
>>>> of
>>>> conductance?
>>>> Thank you for your help in advance.
>>>> Best wishes,
>>>> Gülce 
>>>> 
>>>> Gülce Lale
>>>> MSc Neurosciences
>>>> 
>>>> _______________________________________________
>>>> Simnibs-discuss mailing list
>>>> Simnibs-discuss at drcmr.dk
>>>> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>> 
> 

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