How create a connectome between voxels?

Hi all,

I am new and learning MRtrix from Introduction to MRtrix — Andy’s Brain Book 1.0 documentation (

Finally, I created a connectome that represents the number of streamlines connecting different parts of the brain.

Similarly, can I create a connectome that represents the number of streamlines connecting different voxels of the whole brain? How can I get it specificly?



Hi, you might find this paper helpful: High-resolution connectomic fingerprints: Mapping neural identity and behavior - ScienceDirect. And the code: GitHub - sina-mansour/neural-identity.


Sina’s work linked above specifically looks at vertex connectivity, which we still do not have native support for.

If you’re specifically interested in voxel connectivity, the requisite question is: do you only want endpoint-endpoint connectivity between voxels (acknowledging that surface vertices are a superior manifold for such), or do you want intersection-based connectivity between all voxels, primarily those containing white matter? The latter is IMO closer in concept to the fixel-fixel connectivity matrix used in the FBA pipeline rather than “connectomics”.

Theoretically you could do either by generating a “parcellation” image where each voxel contains a unique integer value, and generating a connectome from that (and indeed, utilising the -assignment_all_voxels option would get you the latter of the cases described above). However I expect this to immediately run out of RAM on any system you could attempt it on, as we do not yet support sparse connectivity matrix generation.


Thanks for your answer.