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Kevin,

The use of network methods is very common in functional neuroscience, and 
several neuroscientists have assembled the brain connectivity toolbox to 
help with this:

 	https://sites.google.com/site/bctnet/

It is available in multiple languages.

If you are also looking for articles about uses of network methods in 
functional neuroscience (you didn't ask, but some of your phrasing 
suggests that as a possible implicit question), Olaf Sporns tends to write 
review articles of various sorts once a year or more, so I would suggest 
recent work by him or one of the review articles he has written jointly 
with Ed Bullmore.

-----
Mason

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  Mason A. Porter
  Professor of Nonlinear and Complex Systems
  Oxford Centre for Industrial and Applied Mathematics
  Mathematical Institute, University of Oxford

  Homepage: http://people.maths.ox.ac.uk/porterm
  Blog: http://masonporter.blogspot.com
  Twitter: @masonporter
  Skype: tepid451
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  "I will be the lion." (Me)
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