Test models and methods when subcortical structures are included

+ There are mechanisms that handled simulations when subcortical structures are present in the model.

See TODO line 621 in simulator.py
This will require testing at the simulator level and then make sure everything work with the framework as well.

I need to investigate a bit more to better described what has to be done

+ Hadnling subcortical structures: https://github.com/pausz/sci_tvb/blob/sandbox/tvb/datatypes/surfaces_scientific.py