@lassoan Thank you. I’m trying out the about-mentioned suggestion on improving the segmentation quality.
But from what I understand, only tree-like structure is returned and the loops /cycles aren’t detected.
EDIT:
It is indeed true. Please check the following excerpt from [vmtk mailing list], written by Luca
Indeed the centerlines filter doesn’t catch loops, which is usually ok for arterial trees, but it can be limiting in other situations such as yours.The reason is that the algorithm searches for some sort of shortest path from the inlet to the outlet, thus is will only choose one of the two arms of the loop.
There are a couple of things you can do:
This is a hack:
a) generate one centerline and save it to a file
b) use vmtksurfaceclipper to make a cut in the branch in which the centerline was generated
c) run vmtkcenterlines again; it will extract the other branch (since the former is not continuous due to the cut); save it to another file
d) use vmtksurfaceappend to have the two centerlines in one dataset, if you need thisuse vmtknetworkextractor; make sure the surface has at least one opening and run the script; this algorithm is less accurate in tracing the centerline, although it might be enough for your needs; however, it handles loops correclty