Dear Alfonso, 

Thank you for your quick response and help!

I have two follow-up questions.

1) I am also interested in whether two groups (patients and controls) differ in terms of connectivity related to the difference between my conditions. I think I can determine this with NBS as well, following the instructions you described above (select both groups, contrast [1 -1], select both conditions [1 -1], hit results explorer, etc)? Can I also use this to determine whether graph measures of the between-condition-difference are correlated with a behavioral measure?

2) Wen selecting both groups  [1 -1]  and both conditions [1 -1], clicking graph theory, specifying edge threshold and desired p-value, I found a difference in global efficiency in paracentral lobule-ROI (PCL_R). Now, the .csv file contained 80 rows (row 1:20 patients 60 Hz, row 21:40 controls 60 Hz, row 41:60 patients 20 Hz, row 61:80 controls 20 Hz). I noticed that when I calculated the difference in global efficiency in PCL_R for condition 60 Hz - 20 Hz, and then performed a two-sample t-test on this difference, I got the same result as provided by the "graph theory" table. 
However, I struggle a bit with the question whether this represents a between-group difference in' global efficiency related to the difference of 60Hz - 20Hz' (of interest), or whether this represents a between-group difference in between-condition differences in global efficiency (cfr. bold text in your response)? 

Kind regards, 
Nina