Hi,
There are two issues that are combining to cause this visualization to look “choppy”.
First, the resolution of the image and the size of the small vessels are nearly the same - as a result, when ConvertTubesToImage is applied and it must decide if a voxel is inside or outside of a vessel, the really small vessels could only partially fill adjacent voxels in such a way that a “gap” seems to appear. This is generally known as “partial voluming”, and slightly blurring and/or dilating an image can help reduce this effect.
Second, the volume rendering transfer function being applied to visualize the image appears to have a sharp step in it that is accentuating the effects of partial voluming. Try smoothing the transfer function to have a more gentle slope and/or move the sharp step to a higher value so that more of the partial voxels are made to appear as “solid” vessel voxels.
Another solution to getting improved visualizations is to convert the .tre file into a VTK surface rendering. That eliminates partial voluming and the need for volume rendering. There is a command-line application included with TubeTK called ConvertTubesToSurface that generates .vtp files from .tre files. It is only available as a command-line tool so it is a bit more challenging to compile and generate it, but I’d be happy to help (perhaps it is best just to send you the executable 
).
Hope this helps,
Stephen