Re: [vmtk-users] centerline extraction problem

[Luca A. <luc...@or...>]

Hi Xiaoli,
 I took a look at your surface. It's not immediately obvious, but there is a whole extra portion of surface inside of it (see screenshot taken with some translucency). This causes the algorithm to basically not work.
I'm not sure how you got to this point, but I suggest you try to re-segment the surface making sure you obtain a single compact 3D model.
Best,

Luca



On Aug 16, 2013, at 3:55 AM, Xiaoli Zhang wrote:

> Hi Luca,
> 
> Attached is the surface file I am working on. The levelset segmentation wasn't working very well on the outer curvature of the arch, but that shouldn't be the problem. Even if I am only working on descending aorta, it still won't work.
> 
> Thanks,
> Xiaoli
> 
> 
> On Thu, Aug 15, 2013 at 5:09 PM, Luca Antiga <luc...@gm...> wrote:
> Hi, I see that there is a jagged line on the surface indicating that the surface is apparently not orientable, so normals flip where you see the dark line (since the shader interpolates normals). You can verify this in Paraview by applying the Glyph filter to the normals.
> 
> This would explain dificulties with the centerline algorithm, since normals are used when extracting the inner Delaunay diagram. 
> 
> Can you send the surface over? I can try to understand what's causing normals to flip.
> 
> Thanks
> 
> Luca
> 
> 
> On 12/ago/2013, at 17:09, Xiaoli Zhang <zha...@gm...> wrote:
> 
>> Hi Luca,
>> 
>> Attached is the screenshots of the surface for centerline extraction from two different views. I have tried not to include aortic arch, but it didn't work either. Any suggestions will be appreciated.
>> 
>> Thanks,
>> Xiaoli
>> 
>> On Sun, Aug 11, 2013 at 4:24 PM, Luca Antiga <luc...@or...> wrote:
>> Hi Xiaoli, 
>>  there must be a Voronoi diagram degeneracy somewhere. Feel free to post a screenshot of the model, I can try to point you to the candidate spots.
>> Best,
>> 
>> Luca
>> 
>> 
>> On Aug 8, 2013, at 7:50 PM, Xiaoli Zhang wrote:
>> 
>>> It seems someone has encountered the same problem before: http://www.mail-archive.com/vmt...@li.../msg00283.html
>>> 
>>> I followed Luca's suggestions apply smoothing (tried passband of 0.01 and 0.1) and add a subdivision step before vmtkcenterlines. Still no luck, vmtkcenterlines script will never return. Any suggestions?
>>> 
>>> On Tue, Aug 6, 2013 at 9:23 PM, Xiaoli Zhang <zha...@gm...> wrote:
>>> I am new to vmtk and I am trying to extract centerline from CT image of the aorta. I prepared the surface in Amira and save as stl (ASCII) format. Then I ran vmtkcenterlines script and place a source point at inlet and a target point at outlet. vmtk then show "computing centerline" and staying for a very long time (>12 hours). The surface I am working on is a small file (stl size <1MB). 
>>> 
>>> Anyone can help please? I can send the screenshot of the surface and stl file if needed. Thanks.
>>> 
>>> Xiaoli
>>> 
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>> 
>> 
>> <C9N3_surface_centerline.jpg>
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> <C9N3.ls.mc.sm.vtp>