VMTK centerline merge does not work

Hello, everyone

I am encountering an issue while merging centerlines using VMTK, and I would appreciate some assistance.

I used the “Extract Centerlines” module in 3D Slicer to extract centerlines from a cerebral vascular mesh and saved it as a VTP file. Next, I loaded the centerlines VTP file in VS Code with Python 3.10 and performed branch splitting using vmtk_branch_splitting. Then, I smoothed the centerlines using vmtk_centerline_smoothing.

Finally, I merged the centerlines from the same vessel using vmtk_centerlinemerge. After merging the centerlines (magenta centerlines) and displaying them using PyVista alongside the pre-merged (smoothed, green centerlines), it is clear that the merged centerlines (magenta) deviate significantly from the original path of the centerlines (green).

The step length during merging was adjusted, but the result did not change. Could you help me identify the cause and suggest improvements?

Here is the code I used:

from vmtk import vmtkscripts
import vtk
def load_vtp(file_name):
    reader = vtk.vtkXMLPolyDataReader()
    polydata = reader.GetOutput()
    return polydata

def vmtk_branch_splitting(centerlines):
    branch_splitting = vmtkscripts.vmtkBranchExtractor()
    branch_splitting.Centerlines = centerlines
    splitted_centerlines = branch_splitting.Centerlines 
    return splitted_centerlines

def vmtk_centerline_smoothing(centerlines, num_iteration=100, smooth_factor=1.2):
    smoother = vmtkscripts.vmtkCenterlineSmoothing()
    smoother.Centerlines = centerlines
    smoother.NumberOfSmoothingIterations = num_iteration 
    smoother.SmoothingFactor = smooth_factor 
    smoothed_centerlines = smoother.Centerlines
    return smoothed_centerlines

def vmtk_centerlinemerge(centerlines, step_length=0.1):  
    centerlinemerge = vmtkscripts.vmtkCenterlineMerge()
    centerlinemerge.Centerlines = centerlines
    centerlinemerge.Length = step_length     
    merged_centerlines = centerlinemerge.Centerlines
    return merged_centerlines 

centerlines = load_vtp("Centerline model.vtp")
radius_array = centerlines.GetPointData().GetArray("Radius")

splitted_centerlines = vmtk_branch_splitting(centerlines) 
smoothed_centerlines = vmtk_centerline_smoothing(splitted_centerlines)
merged_splitted_centerlines = vmtk_centerlinemerge(smoothed_centerlines)

Thank you

After testing by extracting centerlines from only a part of the cerebral vessels, smoothing, and then merging, it worked without any issues.

Next, I thought it might be a problem with the number of inlets, so I used two inlets and specified endpoints partially instead of all of them, and this also worked well.

It seems that increasing the number of endpoints causes an error at some point.

Does anyone have a solution for this?