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This very configurable script allows you to plot a 3D (MNI space) visualisation of a brain graph, with edges represented by cylinders and vertices represented by spheres. To aid orientation, a cortical mesh can be added, as can convex hull outlines.
The colouring and sizing scheme is fully configurable for both edges and vertices.
You can see some example output in
<http://www.ncbi.nlm.nih.gov/pubmed/22677149>
<http://www.ncbi.nlm.nih.gov/pubmed/20541019>
<http://www.ncbi.nlm.nih.gov/pubmed/24562717>
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