Structural connectivity with high-resolution cortical mesh

[Daniele Avitabile]

Dear All,

I am developing a bespoke numerical scheme for brain dynamics and to test it I am looking for a realistic cortical surface mesh (plial, for instance), and a somewhat realistic structural connectivity matrix. I can code in several languages, including python, but I have little familiarity with neuroimaging pipelines.

What I need is:

1. A triangulated surface mesh for a cortex with n vertices (so x,y,z coordinates for the vertices, and corresponding triangulations)

2. An accompanying structural connectivity matrix (hence global connectivity). Ideally, this would be an n-by-n matrix, potentially sparse, expressing some form of functional connectivity between each pair of vertices.

I have seen that the official TVB Data Zenodo repository (https://zenodo.org/records/10128131) has certainly an example of the mesh, in particular in the SurfaceData folder. I have two questions:

* In cortex_2x120k, for instance, I see a mesh that also contains the medial wall, which I would like to remove with some form of masking. Is it possible to obtain a dataset where this has been taken out? Or even a binary file that goes with the vertices, to express which of them are active, and which not?

* The connectivity examples I see in the repository seem fairly small matrices. Is there any dataset containing a connectivity at some of the high resolutions of the SurfaceData folder?

Thanks

Daniele Avitabile

[WOODMAN Michael]

hi,

> a mesh that also contains the medial wall ... Or even a binary file that goes with the vertices, to express which of them are active, and which not?

you can look at the region mapping to identify which vertices can be ignored

> Is there any dataset containing a connectivity at some of the high resolutions of the SurfaceData folder?

Computing vertex-vertex surface connectivity based on DWI is feasible, but simulations tend to be quite slow even with optimized GPU kernels, which is why it's not prevalent.

cheers,
Marmaduke

> On 20 Jul 2026, at 10:22, Daniele Avitabile <d.avi...@gmail.com> wrote:
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[Daniele Avitabile]

Thanks Marmaduke,

In the regionMapping folder, I see files called regionMapping_16k_192. Do I understand correctly that these are corresponding to 16k nodes, and they describe 192 regions? Any pointers to where I can read what ‘region 36’ in that file means? Once again, apologies for the newbie question.

On the connectivity matrix, I completely understand that they are slow to simulate (that’s exactly the type of research I’m doing!). Is there any example at all, even outside of TVB, that you know of?

Best 

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Daniele Avitabile