How to visualize connectivity in 3D brain?

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  • MNE version: 1.3
  • operating system: Windows 10

Hi! guys,
I’m doing connectivity analysis in the source level followed the method in this paper https://www.frontiersin.org/articles/10.3389/fnins.2018.00586/full
The packages used in this paper basically is MNE and conpy(https://users.aalto.fi/~vanvlm1/conpy/), which are very handy :+1:
However, the source level connectivity can only be visualized in a circular graph or a degree map in the brain(the first figure) instead of connectivity in the brain(the second figure).

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I’m wondering if there is some way to visualize the connectivity in the 3D brain, such as extract some node and edge data from the results obtained by mne-connectivity or conpy, then feed to some other visualization software like Brainnet viewer (BrainNet Viewer: A Network Visualization Tool for Human Brain Connectomics).
Thanks a lot! :blush:

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Maybe you can try Nilearn?
https://nilearn.github.io/stable/plotting/index.html

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You have Visbrain (Contents — visbrain 0.4.6 documentation) that gives less fancy 3D brain than with BrainNet :

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But the node/edge etc are highly customizable

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Not exactly what you want, but I used CONN-toolbox to make similar images. It’s a matlab toolbox.

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I tried and it worked! Thanks a lot! :+1: :blush:

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Can you share the code with us? Did you use plot_connectome from nilearn?

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Thanks for the tip! How would you use nilearn to plot MNE connectivity results? I can not figure out how to import a freesurfer parcellation (e.g., lh.aparc.anot and rh.aparc.anot) in nilearn…