Dear Avalon,
In our newest release (https://github.com/softmatterlab/BRAPH-2-Matlab/releases/tag/2.0.0.a3) we added connectivity multiplex pipelines, where the input is an adjacency matrix for each layer per subject.
To understand the structure of the input data, you can check the following tutorial http://braph.org/tutorials/general/connectivity-multiplex-data-format/