Dear Andrew,

I have a question about extracting individual participant connectivity values after running NBS. 

I am running a repeated measures design looking at PRE vs POST effect following an intervention. 

With the aid of your manual I have been able to extract the pairs of nodes (in my case EEG electrodes) with significant connections. 

What I would now like to do is extract the connectivity values for each subject, for each significant connection, so that I have a set of values for each subject that I can use to run further connectivity analyses with behavioral measures etc. 

I have used your example code:

i=1;
j=2; 
global nbs;
nbs = NBS;
N=STATS.N;
ind_upper=find(triu(ones(N,N),1));
cross_ref=zeros(N,N); cross_ref(ind_upper)=1:length(ind_upper);
cross_ref=cross_ref+cross_ref';
ind=cross_ref(i,j);
fprintf('%0.2f\n',GLM.y(:,ind));

I have two questions:

1) As I am using a repeated measures design with 20 subjects in each of the PRE and POST conditions, this code appears to output a list of values for the total number of subjects in my matrix (i.e., 40 (20 pre, 20 post)). Is there a way I can get the difference in connectivity for each connection between the PRE vs POST conditions for the 20 subjects? (I presume this would be the most appropriate measure to use for correlations etc?)

2) when specifying the nodes (i.e., 'i' and 'j' values in the above code) do these just correspond to the row number in the 'node labels' text file I used when running NBS? (e.g., if there was a significant connection between node 7 and node 8 and electrode F7 was the 7th electrode, while F5 was the 8th, then i = 7 and j = 8)? 

Thank you very much for your help.