Plotting publication-quality ball-and-stick models of brain connectivity in 3D I'm working on brain imaging (fMRI) and I'm looking for a way to plot brain effective connectivity (dynamic causal modeling) parameters between different brain regions in a 3D plot. The plotting software should have the following input and output:
Input:
The directed connections from each region to another are defined by a connectivity matrix (no-connections have a value of 0). The 3D coordinates of the brain regions are presented in another matrix, practically using the weighted mean MNI coordinates of the regions as their coordinates for visualization.
Output:
The connection strength would be signaled by the color of the sticks, and/or numerically. However, a first step could be simple 3D ball-and-stick diagram without connection parameters. Output as 2D vector or bitmap image: .ps, .eps, .tex, .png, .jpg, etc. The output would be used in a LaTeX document but also in other formats.

In the field of molecular analysis (with which I'm completely unfamiliar with), I noticed a lot of free and open-source software for creating ball-and-stick plots of molecules (some with publication-quality ray-tracing). Before reinventing the wheel (programming some intermediate software to convert MNI or Talairach 3D coordinates of brain regions to 3D spatial coordinates of atoms and writing them in some molecule file format for molecule ball-and-stick visualization software eg. RasMol to use it for brain connectivity visualization), I want to ask:
Is there a good (and preferibly free) software for brain connectivity visualization?
I have checked the examples of MayaVi, R and TikZ but neither of them has anything related to plotting ball-and-stick visualizations.
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.