Thank you for using Braph, and I am hoping that it would prove to be a useful tool for your research.
It is possible to extract the values of the connectivity matrix, however this method is not currently available through the graphical user interface and you would need to do this through the command line in Matlab. You can accomplish that by doing the following:
A = ga.getA(subject);
where ga_name.fga is the name of the analysis file that you have saved with Braph and subject is the index of the specific subject for which you need the adjacency matrix in the cohort.
If you need the adjacency matrix for a given group g, then you can extract the indices of the subjects in that group by:
indices = find(ga.getCohort.getGroup(1).getProp(Group.DATA)==true);
Then you can extract the matrix for each of those subjects and perform the operation you need.
Hope this helps. If there is anything more I can help you with, please do not hesitate to ask.