"brainGraph" is an R package for performing graph theory analyses of brain MRI data. It is most useful in atlas-based analyses (e.g., using an atlas such as AAL, or one from Freesurfer); however, many of the computations (e.g., the GLM-based functions and the network-based statistic) will work with any graph that is compatible with igraph. The package will perform analyses for structural covariance networks (SCN), DTI tractography (I use probtrackx2 from FSL), and resting-state fMRI covariance (I have used the Matlab-based DPABI toolbox).

In addition to general network operations (available through the R package "igraph"), there is code to perform: bootstrapping, permutation tests, random graph generation, small-worldness/efficiency, robustness/attack analysis, rich-club analysis, and more. There is a GUI for quick data viewing and exploration.

The "Docs" link here on the NITRC page will take you to the User Guide (PDF link) which has detailed information and code blocks examples.