Dear Alfonso,

Reviving an older thread as I am using this code line for my analyses, as I was interested in network connectivity changes related to covariates and groups. I have a couple of questions. 

1) since this analysis uses (uncorrected) two-tailed p-values; however draws from a small pool of regions to test, would it be appropriate to consider the results being adequately corrected with a Bonferroni correction for number of tests, and appropriate choice of number of tails?

Example: I investigate several hypotheses (different covariates/group comparisons) for the connectivity within two networks (SN, DMN) and the connectivity between those two. To obtain a p-value <0.05 per hypothesis, I use a corrected p-value with a Bonferroni correction of 6 (p<0.0083) based on 3 network (SN, DMN, SN-DMN) tests * 2 for two-tailed. 

2) as you explained this gives an average over all ROI connections within each chosen network. But how exactly is the between-network value calculated? As an average of every possible ROI (group1) to ROI (group2) connection? Or a calculated connectivity of the averaged connectivity over all ROIs within each group?