Dear Donald

thank you for the quick reply. This is fascinating. I was asking because I am trying to replicate the same analysis as in http://www.colelab.org/pubs/2013_Cole_NatNeurosci.pdf, specifically their comparison between gPPI and correlation/covariance approach (they mention that they obtained similar results although PPI was better in their case). Maybe I'll ask dr Cole how he dealt with the non symmetrical nature of the adjacency matrix. In theory one could think it as a directed graph... did anyone ever studied gPPI and directed connectivity e.g. using simulated networks? I also like dr Cole's point of regressing out the task to avoid looking at simple co-activations (important especially in block design)

Anyway, I also hope that this will generate some discussion about gPPI and graph theory!

all the best
Enrico