Dear Jason,

The new version of BrainNet Viewer allows to read a matrix with the same size of the edge file. This matrix is to control the color for each single edge. For instance, all the one-directional connections could be labeled as 1, and two-directional connections could be labeled 2. Then in the option panel, the color for label 1 and 2 can be selected separately, just like the module of nodes. 

Best,
Mingrui