Hi Evan,
 it looks like the external delaunay tetrahedra are not properly removed, 
and I think the reason lies with oddly oriented normals at the transition at 
the endcaps.
Anyway, I'd need to have the surface to understand the actual reason and
how to get around it. In the meantime you can try cutting manually, using 
vmtksurfaceclipper.
Cheers

Luca


On Feb 5, 2013, at 11:34 PM, Evan Kao wrote:

> Hello,
> 
> I am having trouble getting vmtkcenterlines to work properly with a specific 
> model.  Using the commands outlined in the tutorials, I opened the endcaps 
> and added flow extensions.  For specific reasons, I imported this surface 
> into a solid modeling software (Rapidform) and remeshed it to smooth out the 
> transitions between the openings and flow extensions.  However, this action 
> closes the endcaps at the end of the flow extensions, so to re-open them I 
> tried using the automatic option in vmtk again.  However, it appears 
> vmtkcenterlines has trouble calculating the centerlines to/from one of the 
> openings, and the result is attached.
> 
> Any ideas about what could be causing this problem and/or how to fix it?
> 
> Thanks for your time,
> Evan Kao
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