Connectivity
Scholarpedia Article on Brain Connectivity
http://www.scholarpedia.org/article/Brain_Connectivity
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This toolbox contains a set of Matlab functions that can be used to analyze neural connectivity patterns. Some of the functions are described in detail in this book chapter:
Sporns, O. (2002) Graph theory methods for the analysis of neural connectivity patterns. Kötter, R. (ed.) Neuroscience Databases. A Practical Guide. Klüwer. PDF
Some of my other relevant papers dealing with neural connectivity analyses (and other subjects) can be found here:
You can find the toolbox at this link: http://www.indiana.edu/~cortex/connectivity_toolbox.html