[FieldTrip] Incorporating White Matter conductivity anisotropy into FEM simbio

Carsten Wolters carsten.wolters at uni-muenster.de
Mon Oct 29 12:31:25 CET 2018

Dear Ravi,

1) You can use the pure SimBio-code from
to treat WM anisotropy.
While it would in principle also be possible to use anisotropic 
conductivities with FieldTrip-SimBio,
this is currently not implemented using ft_prepare_headmodel. Johannes 
(in CC), who implemented
Fieldtrip-SimBio, answered a same question by Junjie Wu in March 2018:
"Depending on your matlab skills and your available time, I could help 
you to give it a
try though. It should be possible with using some direct function calls 
instead of the high-level fieldtrip-functions."

2) We recommend
on individual data. I could imagine that an atlas does a reasonable job 
w.r.t. the main
bigger fiber tracts such as corpus callosum or pyramidal tracts, but 
that the finer details
in the cortices are individual. We always measure T1, T2 and DTI from 
each subject
and I personally do not have experience with such a group-level 
anisotropy compared
to the individual one. Might be interesting to hear from others what 
they think!?


Am 25.10.18 um 23:05 schrieb Ravi Mill:
> Dear Fieldtrippers
> I have applied the FEM simbio head modeling pipeline implemented 
> in Fieldtrip to my EEG data. My understanding is that this pipeline 
> assumes isotropic conductivities for 5 head compartments (as specified 
> by cfg.conductivity in ft_prepare_headmodel). After reading some 
> papers (e.g. Vorwerk et al 2014 
> https://doi.org/10.1016/j.neuroimage.2014.06.040), it seems like 
> incorporating white matter conductivity anisotropy has a relatively 
> small albeit significant effect on the source solution. I am 
> interested in comparing FEM results when treating white matter as 
> anisotropic. My questions are as follows:
>  1. Is there a way to implement the FEM simbio head model whilst
>     treating WM as anisotropic within Fieldtrip? If so, how would one
>     do this (or are there any resources available that demonstrate this)?
>  2. From previous papers and some simbio documentation
>     (https://www.mrt.uni-jena.de/simbio/index.php/SIMBIO/Releasenotes/Examples)
>     it seems like diffusion MRI data is required to calculate the WM
>     conductivity for each individual subject. I only have T1 and T2
>     scans for my subjects. So would it be possible to use WM
>     anisotropic information obtained from some kind of diffusion
>     MRI group average/atlas instead (accepting some loss in
>     subject-level precision)? If so, does such a group average/atlas
>     exist?
> Any help would be greatly appreciated!
> Thanks
> Ravi
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> https://doi.org/10.1371/journal.pcbi.1002202

Prof. Dr.rer.nat. Carsten H. Wolters
University of Münster
Institute for Biomagnetism and Biosignalanalysis
Malmedyweg 15
48149 Münster, Germany

+49 (0)251 83 56904
+49 (0)251 83 56865 (secr.)

+49 (0)251 83 56874

Email: carsten.wolters at uni-muenster.de
Web: https://campus.uni-muenster.de/biomag/das-institut/mitarbeiter/carsten-wolters/

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