[FieldTrip] fieldtrip Digest, Vol 69, Issue 13

[Johannes Vorwerk]

I see. Your missunderstanding is that the dipoles are „represented“ through hexaedrons (and that you need to implement this ;-)). The idea that is usually used to derive FEM for EEG is to stick to the model of a dipole and to represent this dipole through the FEM basis functions. One method to do this (the „Venant approach“) is already implemented in fieldtrip. The way this representation is achieved is described in the papers I mentioned. If you do not want to use a different approach here, no further work on your side is needed.

What you refer to as a „source model“ is what I would call „source space“ (since „source model“ can be easily mixed up…). The source space can be defined just as you would do it for spheres and BEM in fieldtrip. To apply FEM, you have to indicate to fieldtrip to generate a hexahedral head model and „simbio“ as method of forward computation.

Best,
	Johannes

> Am 12.08.2016 um 16:53 schrieb K Jeffrey Eriksen <eriksenj at ohsu.edu>:
> 
> Johannes,
> 
> I an unfamiliar with the derivation you mention (Venant approach) and will read the papers you list here to try to understand it.
> 
> In my naïve view based on thinking about the spherical and BEM cases, the head model is simply a set of 3-4 nested volumes, and in the central volume one implements dipoles at particular locations, which can generally be located anywhere inside the innermost volume. In FEM the entire head volume is hexagons, and I see that FieldTrip/simbio uses a modified (distorted or warped) cubic voxel model for the hexagons. I would presume the simplest idea would be to equate particular gray matter (GM) hexagons with individual dipoles, and perhaps this is what the Venant approach does. 
> 
> I just do not know how to specify particular GM voxels to use as my set of dipoles. How do I address them since they have been distorted from their original cubic voxel shape? Maybe this will be more clear as I read these papers and do some more work with FieldTrip.
> 
> Oh, I guess to me a "source model" is the set of generator locations and orientations. For spheres and BEM these could be point dipoles(1 or 3 per position) or perhaps 2D patches. For FEM these would be tetrahedrons or hexagons with 1 or 3 dipoles at each element used.
> 
> Thanks,
> -Jeff
> 
> Message: 3
> Date: Thu, 11 Aug 2016 19:47:00 -0600
> From: Johannes Vorwerk <j.vorw01 at gmail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] how do embed a dipole model in a FEM head
> 	model?
> Message-ID: <768BFCED-6404-466B-AFC9-F12C3F15FD54 at googlemail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Jeff,
> 
> I am not sure if we have the same understanding of a ?source model?, but in the terminology that is familiar to me there is no need to explicitly define a source model. As source model a current dipole is chosen and by standard the Venant appraoch is implemented to model the current dipole, see for example
> 
> H. Buchner, G. Knoll, M. Fuchs, A. Rienacker, R. Beckmann, M. Wagner, J. Silny, and ? J. Pesch, Inverse localization of electric dipole current sources in finite element models of the human head, Electroencephalography and Clinical Neurophysiology, 102 (1997), pp. 267?278.
> C. H. Wolters, H. Kostler, C. M ? oller, J. H ? ardtlein, and A. Anwander ? , Numerical approaches for dipole modeling in finite element method based source analysis., International Congress Series, 1300 (June 2007), pp. 189?192. ISBN-13:978-0-444-52885-8, http://dx.doi.org/10.1016/j.ics.2007.02.014.
> J. Vorwerk, M. Clerc, M. Burger, and C. H. Wolters, Comparison of boundary element and finite element approaches to the EEG forward problem., Biomedizinische Technik. Biomedical engineering, 57 (2012).
> 
> or http://www.sci.utah.edu/~wolters/PaperWolters/2016/Vorwerk_Dissertation_2016.pdf <http://www.sci.utah.edu/~wolters/PaperWolters/2016/Vorwerk_Dissertation_2016.pdf> where you can also find a basic explanation of the FieldTrip-SimBio pipeline.
> 
> I hope this helps.
> 
> Best,
> 	Johannes
> 
>> Am 11.08.2016 um 18:52 schrieb K Jeffrey Eriksen <eriksenj at ohsu.edu>:
>> 
>> Please ignore my previous request for FEM documentation, as I finally found this:
>> 
>> http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_fem?s[]=simbio 
>> <http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_fem?s%5b%5d=si
>> mbio>
>> 
>> Reading through the above tutorial, there is no mention of how to define a source model to match an FEM head model. I cannot find this using what I consider as reasonable search terms.
>> 
>> Please advise how to create a source model in this case.
>> 
>> Thanks,
>> -Jeff
>> 
> 
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