[FieldTrip] tetrahedral to hexahedral mesh

Johannes Vorwerk j.vorw01 at gmail.com
Wed May 27 10:58:19 CEST 2020

Hi Roberto,

having implemented the FieldTrip-Simbio pipeline and having worked on DBS myself, I would recommend you not to use a hexahedral mesh for this kind of simulations, since it is very hard to properly resolve the geometry of a DBS lead in a hexahedral mesh. Furthermore, the mesh should be especially refined around the DBS lead to achieve high numerical accuracies, which is only (easily) possible using tetrahedral meshes.

To achieve anisotropic conductivities in a tetrahedral mesh, I would recommend you to assign the anisotropy tensor of the voxel closest to the center of the tetrahedral element for each element. Additional interpolation of the tensors is quite tricky.

For DBS computations, I would also recommend you to take a look at LeadDBS (Horn, Andreas, et al. "Lead-DBS v2: Towards a comprehensive pipeline for deep brain stimulation imaging." Neuroimage 184 (2019): 293-316., lead-dbs.org <http://lead-dbs.org/>), which relies on the same numerical background as FieldTrip-SimBio.


> On 27. May 2020, at 10:48, <roberto.garza at artorg.unibe.ch> <roberto.garza at artorg.unibe.ch> wrote:
> Good morning,
> I'm working in the DBS field and I'm using your library to obtain the headmodel. My aim is to include conductivity anisotropy in the computation of the electric field (by using the FieldTrip-SimBio pipeline). I have one conductivity matrix for each voxel in the image, so I built a hexahedral mesh to get a straightforward correspondence between an element and its conductivity. Now I need to integrate in the model the electrode as well: I have it in the form of a tetrahedral mesh. Is there a way to convert tetrahedral mesh to hexahedral? Or is there another way to integrate the two models that I'm not seeing?
> Thank you for your time
> Roberto Garza
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> https://doi.org/10.1371/journal.pcbi.1002202 <https://doi.org/10.1371/journal.pcbi.1002202>
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