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

[Oula Puonti]

Hi Gülce,

You can just take the center coordinate (x,y,z) for the electrode from
the MRI, put that in the GUI (or a script), and project the coordinate
to the skin surface. This will keep the x and y coordinates (more or
less) the same but set the z so that the position is on the skin. After
that, when you define the electrode shape, just add a 2mm gel layer and
that should be it.

Best,
Oula
  

On Wed, 2023-01-25 at 14:15 +0100, Gülce Lale wrote:
> 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
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> > > 
> > 
>