Each of the three matrices represent a distinct network that was found to be signifcant.

It is possible for multiple networks to be signifciant - not just one. 

Originally posted by Ru-Kai Chen:

Dear Andrew

Thank you very much for your answer!

I seem to have a new problem.

When I use NBS to calculate significant connections, I find that at different thresholds, the NBS results file shows different numbers, either 3 or 1. Are they all connections that represent significance? Is there something wrong with this? (Figure below)
Very much looking forward to your answer?