interactive-network

Interactive brain networks

This jupyter notebook generates an interactive brain network graph starting from a connectivity matrix and the related nodes coordinates using plotly. The example data used here are available on the USC Multimodal Connectivity Database. More details available in this post.

To run it, you need python (3.7) and the following packages:

• numpy (1.18.4);
• plotly (4.14.3). To regenerate the brain surface file, freesurfer (6.0.0) is required. The script was tested on macOS 10.15.7.

Some things to keep in mind:

• The script srf2obj is available on Brainder;
• For visualization purposes, only the left half of the brain surface is visualized on top of the graph - despite being qualitatively aligned, one needs to take in mind that the nodes' coordinates and the surface have not been registered;
• More detailed examples on 3D plotting with plotly are available here and here;
• To display the brain surface, the lh.pial file from the FreeSurfer surf folder is first converted to ASCII, then to .obj format and finally is rearranged with a tailored function (as described here); if you have a more direct way to do this, please get in touch!