[FieldTrip] tetrahedral to hexahedral mesh

[Maria Carla Piastra]

Hi all,
following up on this email exchange, I created a pull request you can
follow by adding a comment here:
https://github.com/fieldtrip/fieldtrip/pull/1427
Best,
Maria Carla

On Wed, 27 May 2020 at 10:58, Johannes Vorwerk <j.vorw01 at gmail.com> wrote:

> 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), which relies on the same numerical background as
> FieldTrip-SimBio.
>
> Best,
> Johannes
>
> 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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