While searching for options of connectivity analysis, I found a problem, that when spectral connectivity matrix is exported to excel, cells which were supposed to be zero, have different values (for example, Cz and Cz connectivity isn't 0, but 0,5) while everything else is alright and is the same as in BS. Should I change wrong values on my own in each exported file, or is there anything I should change in BS?
This behaviour is correct. There is no need of change neither in your exported file nor in Brainstorm.
When connectivity matrices are plot in Brainstorm, the diagonal (connectivity with itself) values are seen as Zero to avoid setting the upper limit of the colormap to high values that would conceal the values outside of the diagonal.
This question was already in the forum: Connectivity matrix export