Other features
One thing we have been exploring is the inclusion of tractography visualizations in CVU. The more I play with it, the more I think that visualizing the tractography reconstruction in CVU is not very useful. There exist sophisticated tools for visualizing tractography already, such as TrackVis, that are far more featureful. The idea with tractography in CVU is to visualize tractography and abstract connectivity simultaneously and overlaying one another. However, this tends to produce a cluttered visualization that does little to nothing to ease the burden of interpretation.
Given the difficulties with correctly registering and manipulating tract objects, it's pretty likely that as CVU moves forward I won't do much more with this.
In order to translate from the diffusion space to the surface space, several transformations are required. The diffusion space is specific to each subject. Thus, in order to do this registration properly the subject's specific surface morphology is needed. Thus, whereas I recommend using the fsaverage5 surface for most purposes when visualizing abstract connectivity in CVU, in this case you will first need to load a parcellation using the subject's surface.
And in addition, a B0 volume (registered to the diffusion space) must be provided. When CVU loads the tractography, it will compute the registration between this diffusion space and the anatomical space, and then the registration between the anatomical space and the surface space.
A small minority of subjects have completely incorrect registrations and end up with tractography oriented incorrectly. I have not yet figured out why, but you can hit A and rotate the tractography manually (although this is hard, see Interactor keypresses).
###Color
It's possible in principle to add some color to the tractography visualization. Mayavi has a really bad interface to the VTK colors. So far, my attempts to adjust the colors more finely than with colormaps have only been successful, but they are complete hacks to an interface that is not designed to deal with this. In order to do this reasonably, I would probably submit a set of fixes to mayavi which could take some time to sort through because ideally this would be done for many different VTK sources. I think I will try to do this eventually -- and then maybe add some support for tractography coloring in CVU that is not an absurd hack -- but not anytime soon.