Cool; now that makes more sense.
So, a good option seems to have the individual connectivity matrices in Process 2 (A - B) and then run a Test --> Perm t-test paired.
Is there a way to implement a sliding window for the test (e.g., running the connectivity analyses on 10ms windows rather than on the entire file - and not manually changing the "time window" option?).
Shall that be scripted?