VMTK vessel filtering not working

You can start with simple thresholding, choosing threshold value so low that all vessels that you are interested are included. Then use that for masking and use Grow from seeds. This should allow very clear separation of bone from vessels.

However, if image is noisy and/or low-resolution, contrast filling is uneven, etc. then it may be hard to choose a threshold value that includes small vessels and you may need to do more manual work, e.g., with Paint effect or Draw tubes effect, with thresholding (Maskin settings / editable intensity range).

Do you have a baseline image without contrast? If yes, then you can subtract the background (with automatic motion compensation), which may help in segmenting smaller vessels and automatically remove bone.