Hi Roman,
it's possible that centerlines generated from a surface whose points are
arranged in a very regular lattice might fail due to degeneracies, but this
doesn't happen often at all.
Try to process your discrete marching cubes surface using, e.g.
vmtksurfacetriangles -ifile discretemc.vtp --
Dear Luca,
Is it possible that vmtkcenterlines has problems with surfaces originating from
discrete marching cubes? The surface I had problems with was generated from a
manual segmentation and therefore had no smoothing from normals. I regenerated
a
similar surface from a tomogram with grey-l
Hi Evan,
I checked the models, in fact the jagged endcaps seem to really make a
difference.
I clipped the endcaps using vmtksurfaceclipper (interactively) and centerlines
succeed.
I checked to see if the surface had spurious holes (it doesn't) or non-manifold
edges
(it doesn't either), so I'm
Hi Roman,
can you please send me the incriminated surface?
Thanks
Luca
On Feb 13, 2013, at 3:36 PM, Dr. Roman Grothausmann wrote:
> Dear mailing list members,
>
>
> vmtkcenterlines segfaults with a specific data-set of mine. It works all fine
> with similar data-sets. I generally get a lot
Dear mailing list members,
vmtkcenterlines segfaults with a specific data-set of mine. It works all fine
with similar data-sets. I generally get a lot of
Generic Warning: In
/home/grothama/programme/vmtk-1.0.1/build_iana0_130211/VTK/Common/vtkMath.cxx,
line 553
Unable to factor linear system
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 c
Hi Michael,
unfortunately this is a bug that got overlooked in the last major release, so
it's not fixed yet.
The result with two sources is exactly the same as tracing twice with 1 source
point and 3 end points each time:
vmtksurfacesmoothing -ifile source.stl -passband 0.01 -iterations 30 --pi
Hi,
Does vmtk centerlines script work for multiple source points?
I am loading stl mesh, and them selecting 2 source points and 3 end points.
After the computing there are only centerlines from one source point in my vtp
data. I am using that command:
vmtksurfacesmoothing -ifile source.stl -p
Hi Eduardo,
it looks like point 13910 doesn't exist on the surface. How many vertices does
the surface have?
From the error, it looks like the surface has less than 13911 points.
Best regards
Luca
On Aug 10, 2012, at 3:18 PM, Eduardo - Yahoo wrote:
> Hi everyone!
>
> I am trying to run vmtk
Hi everyone!
I am trying to run vmtkcenterlines.py with some parameters but I can`t. I
am using this command line
*"vmtkcenterlines -seedselector idlist -sourceids 13910 -targetids 1054
13908 13907 -ifile ./Pasta/id1/id1_model.vtp -endpoints 1 --pipe
vmtkcenterlineresampling -length 0.1 -ofile ./P
Hi Sergio,
indeed I've looked into it and I can get a network using vmtk 1.0.0 (which
doesn't
get stuck when it can't trace a line - it simply skips it).
I just need some more time for understanding why I don't get a few of the
branches,
I'll keep you posted.
Thanks for the patience and for the
Dear Luca,
Have you been able to see the vtp file or perhaps this has been blocked by
the list?
Please, let me know if you need the file.
Best regards
On Mon, May 7, 2012 at 4:32 PM, Sergio Vera wrote:
> Hello Luca,
>
> Thanks for your reply. I've tried to subdivide the surface as you told
>
Dear Sergio,
is it possible that your surface has a very low density (in terms of surface
triangles)?
In this case you could try to subdivide the surface right after marching cubes:
vmtkmarchingcubes -ifile c:\\work\\batch\\ABD-Vascular-seg.mha -l 0.5 --pipe
vmtksurfacesubdivision -method loop
Hello
I'm want to extract centerlines from an abdominal aorta and illiacs. The
following pypes script
vmtkmarchingcubes -ifile c:\\work\\batch\\ABD-Vascular-seg.mha -l 0.5
--pipe vmtksurfacesmoothing -passband 0.1 -iterations 30 --pipe
vmtksurfaceclipper --pipe vmtkcenterlines -seedselector openpr
Hi Lingfeng,
for those cases you might want to add a subdivision step right before
centerlines (note that this might lead to a large surface and longer
computation times):
vmtksurfaceconnectivity -ifile airway.vtp --pipe vmtksurfacesmoothing -passband
0.01 -iterations 30 --pipe vmtksurfacesubd
Thank you Luca,
It is much better than before. In most cases, it can produce
centerline. However, if I select all branch distal points, it would
not return.
Does vmtk support timeout? If the time took for calculating centerline
between two points is longer than expected, vmtk will ignore the two
Hi Linfeng,
the surface probably leads to degenerate Voronoi polygons somewhere in the
smaller branches.
Try smoothing the surface first, using
vmtksurfacesmoothing -ifile airway.vtp -passband 0.01 -iterations 30 -ofile
airway_smooth.vtp
maybe try with -passband 0.1 if the smoothing is too stro
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