[vmtk-users] centerlines question

[Joong-Ho W. <jh...@st...>]

Hi,

I compiled and installed vmtk0.6 on a Windows XP machine. It seems work 
fine, but I have a trouble with using vmtkcenterlines.

I want to extract centerlines of the abdominal aorta and its branches. 
As a simple test, I segmented the aorta (below the heart and above the 
iliac bifurcation) and the right renal artery from a CTA data, resulting 
in a T-shaped branching. Then I obtained a surface model using 
vmtkmarchingcubes (I basically followed the tutorial in the website).

Next, I ran vmtkcenterlines:

vmtkcenterlines.py -ifile p001_part1_model.vtp -ofile 
p001_part1_centerlines2.vtp

as in the tutorial.

As I wanted T-shaped centerlines, I thought that I need two pairs of 
source and target points. I chose both source points to be the same: the 
proximal endpoint of the aorta. Target points are chosen to be the 
distal end of the aorta and the end of the renal artery.

Since the model is a closed surface, I pressed space *twice* on the top 
of the aorta surface to select the source points. For target points I 
pressed space on two different points on the surface, of course.

During centerline extraction, a vtkOutputWindow popped up and complained :

Unable to factor linear system

which was a vmtkMath error.

When I displayed the centerlines (p001_part1_centerlines2.vtp, using 
vmtkcenterlineviewer), I only see a single centerline, which I guess is 
one for the aorta.

I tried again with only a single source point, but the result was the same.

Interestingly, the Voronoi diagram looked fine.

To summarize,

1. I can't see multiple centerlines.
2. I have no confidence on my selection of source and target points 
(what is the precise definition of these points?)

It appears that I made some simple mistake, but can't guess what it is.
FYI, I attach the output of vmtkcenterlines below. It seems that the 
script produces only one centerline.

Thanks in advance,

Joong-Ho.



C:\Program Files\VMTK\bin>vmtkcenterlines.py -ifile p001_part1_model.vtp -of
p001_part1_centerlines2.vtp

Creating vmtkCenterlines instance.
Automatic piping vmtkcenterlines
Parsing options vmtkcenterlines
     SurfaceInputFileName = p001_part1_model.vtp
     CenterlinesOutputFileName = p001_part1_centerlines2.vtp
Explicit piping vmtkcenterlines
Input vmtkcenterlines members:
     Id = 0
     Surface = None
     SurfaceInputFileName = p001_part1_model.vtp
     SeedSelectorName = pickpoint
     SourceIds = []
     TargetIds = []
     SourcePoints = []
     TargetPoints = []
     AppendEndPoints = 0
     FlipNormals = 0
     CapDisplacement = 0.1
     RadiusArrayName = MaximumInscribedSphereRadius
     AppendEndPoints = 0
     Resampling = 0
     ResamplingStepLength = 1.0
     DelaunayTessellation = None
     UseTetGen = 0
     TetGenDetectInter = 1
     CostFunction = 1/R
     CenterlinesOutputFileName = p001_part1_centerlines2.vtp
     DelaunayTessellationOutputFileName =
     VoronoiDiagramOutputFileName =
Reading VTK XML surface file.
Executing vmtkcenterlines ...
NonManifold check.
Cleaning surface.
Triangulating surface.
Capping surface.
Please position the mouse and press space to add source points, 'u' to undo
Please position the mouse and press space to add target points, 'u' to undo
Computing centerlines.
Done executing vmtkcenterlines.
Writing VTK XML surface file.
Output vmtkcenterlines members:
     Id = 0
     Centerlines = vtkPolyData
     RadiusArrayName = MaximumInscribedSphereRadius
     EikonalSolutionArrayName = EikonalSolutionArray
     EdgeArrayName = EdgeArray
     EdgePCoordArrayName = EdgePCoordArray
     CostFunctionArrayName = CostFunctionArray
     DelaunayTessellation = vtkUnstructuredGrid
     VoronoiDiagram = vtkPolyData
     PoleIds = vtkIdList