Dear Andrew, 

Thank you for your quick response. I'm running the analysis with 500.000 permutations, it just takes ages... Thanks for the warning.

I replaced the excluded node-values to zero, but still nothing seems to change. I attached the nbs structures for the full matrix and selected matrix in a zip file. Can you tell me if the selection is correct? Maybe I'm just missing something?

I am interested in testing connectivity from network e.g. A (7 regions) to network A, B, C and D. This should reduce the nr of comparisons to 581 (7*84 regions) compared to 3486 when using the full matrix (84x84 regions). 

For this, I kept all rows and columns of network A (see datafile attached) in the matrix and set al other edges to zero, I also tried with only keeping the rows, but that gives the same results too. I now see that e.g. all test_stats are zero for those edges that I excluded, but the size of these matrices (e.g. nbs.GLM.y or nbs.NBS.test_stat) have not changed. Is their any way I can check final number of comparisons that the program uses for correction?

Best, Marieke