Plotting publication-quality ball-and-stick models of brain connectivity in 3D
Have you tried:


connectomeviewer http://www.connectomeviewer.org/viewer
brainnetviewer  http://www.nitrc.org/projects/bnv/ which is a toolbox for the SPM software package http://www.fil.ion.ucl.ac.uk/spm/
Gephi http://gephi.org/
Trackvis http://trackvis.org/


Also Nico Dosenbach has some amazing picture of brain connectivity in this paper http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135376/. The code is based on matlab and the plotting can be done in the caret software http://brainvis.wustl.edu/wiki/index.php/Main_Page from the Van-Essen Lab.