Dear Che,
I double checked the matrices you sent me and it seems that you were trying to upload the time series for the individual regions instead of uploading pre-calculated adjacency matrices. Therefore, as the matrices that you uploaded were not square matrices Braph returned an error.
I checked and you can calculate adjacency matrices (without error) if you use the correlation coefficients offered in Braph, and you do not need the modified version. However, if you pre-calculate your adjacency matrices, then you can upload and analyze them via the modified version of Braph that I provided.
Hope this helps. Please let me know if this problem remains for you and how I can further help you.
Best,
Mite