[vtkusers] Re : Build 3D Mesh from vtkImageData using vtkMarchingCubes - holes filling ?

[Malsoaz James]

Thank you Bill for your answer.

The input vtkImageData is the result of a segmentation process. Sometimes, the segmentation is not perfect, part of the object can be missing on a slice. For now, I can't know automatically if a slice is missing or not before the 3D build. Thus, I can't create it manually. I thought Marching cubes was able to deal with this kind of problem, apparently not.

I will look at your solution and let you know.

In any case, the resampler solution works, it is just not really suitable for bad resolution.

Best.



________________________________
 De : Bill Lorensen <bill.lorensen at gmail.com>
À : Malsoaz James <jmalsoaz at yahoo.fr> 
Cc : "vtkusers at vtk.org" <vtkusers at vtk.org> 
Envoyé le : Mardi 6 Décembre 2011 18h19
Objet : Re: [vtkusers] Build 3D Mesh from vtkImageData using vtkMarchingCubes - holes filling ?
 
Another possible solution is to convert your image data to a
rectilinear grid. The rectilinear grid supports non uniform spacing.
Once converted you would use vtkContourFilter rather than Marching
Cubes. It will be slower.

Bill

On Tue, Dec 6, 2011 at 12:16 PM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
> Marching Cubes is the correct filter and your results look good
> (except for the missing slice. You could try to create a missing slice
> by creating a new slice. Maybe by averaging the slice above and below
> the missing slice.
>
> Why is the data missing?
>
> On Tue, Dec 6, 2011 at 12:03 PM, Malsoaz James <jmalsoaz at yahoo.fr> wrote:
>> Dear VTK users
>>
>> I'm trying to build a 3D mesh from a vtkImageData using vtkMarchingCubes.
>> The vtkImageData is build from a list of 2D binary slices.
>>
>> vtkMarchingCubes works great. But when a slice(s) is(are) missing, it
>> creates a hole in the 3D mesh (see image in attachment).
>>
>> 1 - How can I fill this kind of hole ? Ideally, I would like to link the two
>> parts of the mesh
>>
>> 2 - I found a solution in the use of a resampler (vtkImageResample,
>> vtkImageShrink3D, don't know which one is recommanded). Unfortunately, it
>> sometimes produces ugly mesh with "stair effect" when the spacing is too big
>> (still there after decimate and smooth). Is it a good solution ? How to
>> solve the stair problem ?
>>
>> 3 - Browsing the mailing list brings me to the notion of "repair hole" for
>> marching cubes. I don't know a lot about it. But should I look into this ?
>> Some solutions exist for this such as http://www.opentopology.org/
>>
>> 4 - Is vtkMarchingCubes the class I should use for my purpose or should I
>> look at vtkVoxelContoursSurfaceFilter or any other filter ?
>>
>>
>> Thank you for you help.
>> Best.
>>
>>
>>
>>
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>
>
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