Chapter 2: Features of Complex Networks
There are various toolboxes for network analysis but the most widely used is the Brain Connectivity Toolbox. While being developed in Matlab, many functions are also available in C++. The toolbox contains a collection of complex network measures and large-scale neuroanatomical connectivity datasets.
Matlab code for generating hierarchical networks can be found here. These routines were used for the article Marcus Kaiser and Claus Hilgetag (2010). Optimal hierarchical modular topologies for producing limited sustained activation of neural networks. Frontiers in Neuroinformatics (PDF)