It happens sometimes that the 3D scene being visualized will vanish from the rendering window. It seems to be sensitive to certain ROIs (Nifti/Analyze), but I do not know what characteristics of the ROI cause it to happen. Using View::Reset will bring the visualization back, but when it is rotated away from the reset state, it vanishes again.
One workaround that can help is to File::Replace Track with the same .trk file. This works about 75% of the time.
This is a mysterious bug that I am still trying to fix (or at least to reproduce). The workaround is turn off "Object Annotations" (Overview->Settings).
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