During the study of diffusion imaging and after connectome extraction by MRTRIX3, I tried to calculate the topological features.
I followed the following document “” “Full title: A hands-on tutorial on network and topological neuroscience 2 Short title: Hands-on network and topological neuroscience” “”.
When I use the python codes in there, I noticed that the results are different from those already calculated by bct.

different from
Code example

Compute clustering coefficient of the network

nx.clustering (G_gt, weight = ‘weight’)

Compute the average clustering coefficient of the network

nx.average_clustering (G_gt, weight = ‘weight’)
I wanted to know what I need to do to make it have the same results, so I am wondering if the connectome made by MRTRIX3 is a correlation matrix (which is the case for the connectivity matrix for functional MRI )


I have to admit I’ve no idea about these toolboxes… I assume the document you’re referring to is this one? Either way, this probably isn’t the right forum to ask for support with these packages. But regarding your final question:

No, the structural connectome obtained using tractography is not (usually) a correlation matrix. If you follow our recommended pipelines, you’ll actually end up with something indicative of the amount of white matter connecting between the two regions. I don’t know how that would influence your analysis though…

All the best,