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The analyses mostly use python code with AFNI and R functions. The bct package for R is required to run these.
Further documentation by Sarah Kenny (the bct package author) is here.

Analyses

Modularity

This is to assess network structures or graphs. Graphs are sets of nodes and edges. Here, voxels are "nodes" and the connection between them is an "edge." So, we can represent and analyze the brain network as a graph. The analysis measures the network's partitioning into modules - or communities. A community is a densely connected set of nodes.

Degree

How many connections does this voxel have? That is its "degree."

Node roles

Nodes (voxels, vertices, etc.) have roles in the network. For example, Guimera & Amaral suggest seven universal roles...