Self connection of a region to itself in connectome.csv

Dear MRtrix3 community,

I extracted connectomes of a few subjects (downloaded from HCP) by following the MRtrix3 guideline.

I am not sure whether my question is appropriate to ask here… but my question is that when I checked output connectome.csv files, I realized that a relatively large number of streamlines (about 30~40% of total streamlines) are connecting a region to itself (self-connection).

For the further analysis of the connectome, do I set those self-connections to zero or keep it?


Hi @bwlee89,

If you are interested in studying inter-areal structural connectivity, typically self-connections are not taken into account. So yes, you can set the diagonal values to zero.

P.S. You can also provide -zero_diagonal to achieve this end when using the tck2connectome command.