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

[Oula Puonti]

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
> > > 
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>