Using itkDeformableSimplexMesh3DFilter

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Using itkDeformableSimplexMesh3DFilter

Dan Chang
Hi all.
I am trying to make a CLI module that uses itkDeformableSimplexMesh3DFilter
to create a deformable surface model from label maps.

As the first step, I am trying to test if this example [1] could be
replicated in Slicer. I have used the Extension creater module to generate a
CLI module. However, I get [2] error on the line

SimplexFilterType::Pointer simplexFilter = SimplexFilterType::New();  

Another question is how to feed the labelmap to this filter. I currently am
thinking to do something similar in this example [3]. Am I headed in the
right direction?

Thanks in advance!


[1]
http://www.na-mic.org/svn/Slicer3-lib-mirrors/trunk/Insight/Testing/Code/Algorithms/itkDeformableSimplexMesh3DFilterTest.cxx

[2] error LNK2019: unresolved external symbol "public: __cdecl
itk::SimplexMeshGeometry::~SimplexMeshGeometry(void)"
(??1SimplexMeshGeometry@itk@@QEAA@XZ) referenced in function "protected:
virtual __cdecl itk::SimplexMesh<double,3,class
itk::DefaultDynamicMeshTraits&lt;double,3,3,double,double,double>
>::~SimplexMesh<double,3,class
itk::DefaultDynamicMeshTraits&lt;double,3,3,double,double,double> >(void)"
(??1?$SimplexMesh@N$02V?$DefaultDynamicMeshTraits@N$02$02NNN@itk@@@itk@@MEAA@XZ)
D:\Dropbox\Slicer\dev\CLI\DeformableMesh460\DeformableSimplexMesh\DeformableSimplexMesh.obj
DeformableSimplexMeshLib

[3]
https://github.com/SlicerProstate/SlicerProstate/blob/master/SegmentationSmoothing/SegmentationSmoothing.cxx



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Re: Using itkDeformableSimplexMesh3DFilter

lasso2
> I get [2] error

You need to start from a CLI module that you generate by the Extension Wizard module in Slicer. The generated module already uses an ITK filter, so it should work for any other filter, just make sure to list the correct ITK components in CMakeLists.txt.

> Am I headed in the right direction?
Maybe. What would you like to do?

Andras

-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Dan Chang
Sent: April 7, 2017 12:42
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] Using itkDeformableSimplexMesh3DFilter

Hi all.
I am trying to make a CLI module that uses itkDeformableSimplexMesh3DFilter to create a deformable surface model from label maps.

As the first step, I am trying to test if this example [1] could be replicated in Slicer. I have used the Extension creater module to generate a CLI module. However, I get [2] error on the line

SimplexFilterType::Pointer simplexFilter = SimplexFilterType::New();  

Another question is how to feed the labelmap to this filter. I currently am thinking to do something similar in this example [3]. Am I headed in the right direction?

Thanks in advance!


[1]
http://www.na-mic.org/svn/Slicer3-lib-mirrors/trunk/Insight/Testing/Code/Algorithms/itkDeformableSimplexMesh3DFilterTest.cxx

[2] error LNK2019: unresolved external symbol "public: __cdecl itk::SimplexMeshGeometry::~SimplexMeshGeometry(void)"
(??1SimplexMeshGeometry@itk@@QEAA@XZ) referenced in function "protected:
virtual __cdecl itk::SimplexMesh<double,3,class itk::DefaultDynamicMeshTraits&lt;double,3,3,double,double,double>
>::~SimplexMesh<double,3,class
itk::DefaultDynamicMeshTraits&lt;double,3,3,double,double,double> >(void)"
(??1?$SimplexMesh@N$02V?$DefaultDynamicMeshTraits@N$02$02NNN@itk@@@itk@@MEAA@XZ)
D:\Dropbox\Slicer\dev\CLI\DeformableMesh460\DeformableSimplexMesh\DeformableSimplexMesh.obj
DeformableSimplexMeshLib

[3]
https://github.com/SlicerProstate/SlicerProstate/blob/master/SegmentationSmoothing/SegmentationSmoothing.cxx



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Re: Using itkDeformableSimplexMesh3DFilter

Dan Chang
In reply to this post by Dan Chang
Hi Andras.
Thanks for the advice.

Listing the ITK components in CMakeLists.txt fixed the problem. It might be good to add this information somewhere here [1] CLI part?

The ModelMaker module uses the MarchingCubes algorithm, but it is not giving a good result for largely spaced image sets that I would like to reconstruct. Was exploring the idea to wrap a surface around the label maps and see how the results are. Wasn't sure how to feed the labelmap to the ITK pipeline.

Thanks.


On Fri, Apr 7, 2017 at 3:08 PM, Andras Lasso <[hidden email]> wrote:
> I get [2] error

You need to start from a CLI module that you generate by the Extension Wizard module in Slicer. The generated module already uses an ITK filter, so it should work for any other filter, just make sure to list the correct ITK components in CMakeLists.txt.

> Am I headed in the right direction?
Maybe. What would you like to do?

Andras

-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Dan Chang
Sent: April 7, 2017 12:42
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] Using itkDeformableSimplexMesh3DFilter

Hi all.
I am trying to make a CLI module that uses itkDeformableSimplexMesh3DFilter to create a deformable surface model from label maps.

As the first step, I am trying to test if this example [1] could be replicated in Slicer. I have used the Extension creater module to generate a CLI module. However, I get [2] error on the line

SimplexFilterType::Pointer simplexFilter = SimplexFilterType::New();

Another question is how to feed the labelmap to this filter. I currently am thinking to do something similar in this example [3]. Am I headed in the right direction?

Thanks in advance!


[1]
http://www.na-mic.org/svn/Slicer3-lib-mirrors/trunk/Insight/Testing/Code/Algorithms/itkDeformableSimplexMesh3DFilterTest.cxx

[2] error LNK2019: unresolved external symbol "public: __cdecl itk::SimplexMeshGeometry::~SimplexMeshGeometry(void)"
(??1SimplexMeshGeometry@itk@@QEAA@XZ) referenced in function "protected:
virtual __cdecl itk::SimplexMesh<double,3,class itk::DefaultDynamicMeshTraits&lt;double,3,3,double,double,double>
>::~SimplexMesh<double,3,class
itk::DefaultDynamicMeshTraits&lt;double,3,3,double,double,double> >(void)"
(??1?$SimplexMesh@N$02V?$DefaultDynamicMeshTraits@N$02$02NNN@itk@@@itk@@MEAA@XZ)
D:\Dropbox\Slicer\dev\CLI\DeformableMesh460\DeformableSimplexMesh\DeformableSimplexMesh.obj
DeformableSimplexMeshLib

[3]
https://github.com/SlicerProstate/SlicerProstate/blob/master/SegmentationSmoothing/SegmentationSmoothing.cxx



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Re: Using itkDeformableSimplexMesh3DFilter

Dzenan Zukic
Hi Dan,

you might want to use ITK's remote module called Cuberille:

Regards

Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

On Fri, Apr 7, 2017 at 3:34 PM, Dan <[hidden email]> wrote:
Hi Andras.
Thanks for the advice.

Listing the ITK components in CMakeLists.txt fixed the problem. It might be good to add this information somewhere here [1] CLI part?

The ModelMaker module uses the MarchingCubes algorithm, but it is not giving a good result for largely spaced image sets that I would like to reconstruct. Was exploring the idea to wrap a surface around the label maps and see how the results are. Wasn't sure how to feed the labelmap to the ITK pipeline.

Thanks.


On Fri, Apr 7, 2017 at 3:08 PM, Andras Lasso <[hidden email]> wrote:
> I get [2] error

You need to start from a CLI module that you generate by the Extension Wizard module in Slicer. The generated module already uses an ITK filter, so it should work for any other filter, just make sure to list the correct ITK components in CMakeLists.txt.

> Am I headed in the right direction?
Maybe. What would you like to do?

Andras

-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Dan Chang
Sent: April 7, 2017 12:42
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] Using itkDeformableSimplexMesh3DFilter

Hi all.
I am trying to make a CLI module that uses itkDeformableSimplexMesh3DFilter to create a deformable surface model from label maps.

As the first step, I am trying to test if this example [1] could be replicated in Slicer. I have used the Extension creater module to generate a CLI module. However, I get [2] error on the line

SimplexFilterType::Pointer simplexFilter = SimplexFilterType::New();

Another question is how to feed the labelmap to this filter. I currently am thinking to do something similar in this example [3]. Am I headed in the right direction?

Thanks in advance!


[1]
http://www.na-mic.org/svn/Slicer3-lib-mirrors/trunk/Insight/Testing/Code/Algorithms/itkDeformableSimplexMesh3DFilterTest.cxx

[2] error LNK2019: unresolved external symbol "public: __cdecl itk::SimplexMeshGeometry::~SimplexMeshGeometry(void)"
(??1SimplexMeshGeometry@itk@@QEAA@XZ) referenced in function "protected:
virtual __cdecl itk::SimplexMesh<double,3,class itk::DefaultDynamicMeshTraits&lt;double,3,3,double,double,double>
>::~SimplexMesh<double,3,class
itk::DefaultDynamicMeshTraits&lt;double,3,3,double,double,double> >(void)"
(??1?$SimplexMesh@N$02V?$DefaultDynamicMeshTraits@N$02$02NNN@itk@@@itk@@MEAA@XZ)
D:\Dropbox\Slicer\dev\CLI\DeformableMesh460\DeformableSimplexMesh\DeformableSimplexMesh.obj
DeformableSimplexMeshLib

[3]
https://github.com/SlicerProstate/SlicerProstate/blob/master/SegmentationSmoothing/SegmentationSmoothing.cxx



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Re: Using itkDeformableSimplexMesh3DFilter

lasso2
In reply to this post by Dan Chang

This is a common problem and typically addressed at three levels:

  • If imaging data is acquired for 3D modeling then always ask for using imaging protocols that provide images with isotropic spacing (similar in-slice pixel spacing as spacing between slices). You can use highly anisotropic images, too, you just won’t be able to benefit much from the high in-plane resolution.
  • Crop and resample your grayscale volume at isotropic spacing before starting segmentation on it. Crop volume module is developed exactly for this purpose. Choose isotropic spacing and bspline kernel options.
  • Use segment editor’s built-in binary labelmap to closed surface converter. It applies low-pass filtering, which removes staircase artifacts.

 

In the future we plan to improve level 2 and 3, by offering optional isotropic resampling of the master volume in segment editor; and making segment editor effects work on fractional labelmaps (not just on binary labelmaps).

 

Andras

 

From: Dzenan Zukic [mailto:[hidden email]]
Sent: April 7, 2017 16:19
To: Dan <[hidden email]>
Cc: Andras Lasso <[hidden email]>; SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-devel] Using itkDeformableSimplexMesh3DFilter

 

Hi Dan,

 

you might want to use ITK's remote module called Cuberille:

 

Regards


Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

 

On Fri, Apr 7, 2017 at 3:34 PM, Dan <[hidden email]> wrote:

Hi Andras.

Thanks for the advice.

 

Listing the ITK components in CMakeLists.txt fixed the problem. It might be good to add this information somewhere here [1] CLI part?

 

The ModelMaker module uses the MarchingCubes algorithm, but it is not giving a good result for largely spaced image sets that I would like to reconstruct. Was exploring the idea to wrap a surface around the label maps and see how the results are. Wasn't sure how to feed the labelmap to the ITK pipeline.

 

Thanks.

 

 

On Fri, Apr 7, 2017 at 3:08 PM, Andras Lasso <[hidden email]> wrote:

> I get [2] error

You need to start from a CLI module that you generate by the Extension Wizard module in Slicer. The generated module already uses an ITK filter, so it should work for any other filter, just make sure to list the correct ITK components in CMakeLists.txt.

> Am I headed in the right direction?
Maybe. What would you like to do?

Andras


-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Dan Chang
Sent: April 7, 2017 12:42
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] Using itkDeformableSimplexMesh3DFilter

Hi all.
I am trying to make a CLI module that uses itkDeformableSimplexMesh3DFilter to create a deformable surface model from label maps.

As the first step, I am trying to test if this example [1] could be replicated in Slicer. I have used the Extension creater module to generate a CLI module. However, I get [2] error on the line

SimplexFilterType::Pointer simplexFilter = SimplexFilterType::New();

Another question is how to feed the labelmap to this filter. I currently am thinking to do something similar in this example [3]. Am I headed in the right direction?

Thanks in advance!


[1]
http://www.na-mic.org/svn/Slicer3-lib-mirrors/trunk/Insight/Testing/Code/Algorithms/itkDeformableSimplexMesh3DFilterTest.cxx

[2] error LNK2019: unresolved external symbol "public: __cdecl itk::SimplexMeshGeometry::~SimplexMeshGeometry(void)"
(??1SimplexMeshGeometry@itk@@QEAA@XZ) referenced in function "protected:
virtual __cdecl itk::SimplexMesh<double,3,class itk::DefaultDynamicMeshTraits&lt;double,3,3,double,double,double>
>::~SimplexMesh<double,3,class
itk::DefaultDynamicMeshTraits&lt;double,3,3,double,double,double> >(void)"
(??1?$SimplexMesh@N$02V?$DefaultDynamicMeshTraits@N$02$02NNN@itk@@@itk@@MEAA@XZ)
D:\Dropbox\Slicer\dev\CLI\DeformableMesh460\DeformableSimplexMesh\DeformableSimplexMesh.obj
DeformableSimplexMeshLib

[3]
https://github.com/SlicerProstate/SlicerProstate/blob/master/SegmentationSmoothing/SegmentationSmoothing.cxx



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Re: Using itkDeformableSimplexMesh3DFilter

Dan Chang
In reply to this post by Dan Chang
Thanks for the suggestions. I will tryout both options. One problem with resampling is that the images are highly discontinuous. (2mm step of prostate cross-sections) 
Thanks again.

On Sat, Apr 8, 2017 at 8:07 AM, Andras Lasso <[hidden email]> wrote:

This is a common problem and typically addressed at three levels:

  • If imaging data is acquired for 3D modeling then always ask for using imaging protocols that provide images with isotropic spacing (similar in-slice pixel spacing as spacing between slices). You can use highly anisotropic images, too, you just won’t be able to benefit much from the high in-plane resolution.
  • Crop and resample your grayscale volume at isotropic spacing before starting segmentation on it. Crop volume module is developed exactly for this purpose. Choose isotropic spacing and bspline kernel options.
  • Use segment editor’s built-in binary labelmap to closed surface converter. It applies low-pass filtering, which removes staircase artifacts.

 

In the future we plan to improve level 2 and 3, by offering optional isotropic resampling of the master volume in segment editor; and making segment editor effects work on fractional labelmaps (not just on binary labelmaps).

 

Andras

 

From: Dzenan Zukic [mailto:[hidden email]]
Sent: April 7, 2017 16:19
To: Dan <[hidden email]>
Cc: Andras Lasso <[hidden email]>; SPL Slicer Devel <[hidden email]>
Subject: Re: [slicer-devel] Using itkDeformableSimplexMesh3DFilter

 

Hi Dan,

 

you might want to use ITK's remote module called Cuberille:

 

Regards


Dženan Zukić, PhD, Senior R&D Engineer, Kitware (Carrboro, N.C.)

 

On Fri, Apr 7, 2017 at 3:34 PM, Dan <[hidden email]> wrote:

Hi Andras.

Thanks for the advice.

 

Listing the ITK components in CMakeLists.txt fixed the problem. It might be good to add this information somewhere here [1] CLI part?

 

The ModelMaker module uses the MarchingCubes algorithm, but it is not giving a good result for largely spaced image sets that I would like to reconstruct. Was exploring the idea to wrap a surface around the label maps and see how the results are. Wasn't sure how to feed the labelmap to the ITK pipeline.

 

Thanks.

 

 

On Fri, Apr 7, 2017 at 3:08 PM, Andras Lasso <[hidden email]> wrote:

> I get [2] error

You need to start from a CLI module that you generate by the Extension Wizard module in Slicer. The generated module already uses an ITK filter, so it should work for any other filter, just make sure to list the correct ITK components in CMakeLists.txt.

> Am I headed in the right direction?
Maybe. What would you like to do?

Andras


-----Original Message-----
From: slicer-devel [mailto:[hidden email]] On Behalf Of Dan Chang
Sent: April 7, 2017 12:42
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] Using itkDeformableSimplexMesh3DFilter

Hi all.
I am trying to make a CLI module that uses itkDeformableSimplexMesh3DFilter to create a deformable surface model from label maps.

As the first step, I am trying to test if this example [1] could be replicated in Slicer. I have used the Extension creater module to generate a CLI module. However, I get [2] error on the line

SimplexFilterType::Pointer simplexFilter = SimplexFilterType::New();

Another question is how to feed the labelmap to this filter. I currently am thinking to do something similar in this example [3]. Am I headed in the right direction?

Thanks in advance!


[1]
http://www.na-mic.org/svn/Slicer3-lib-mirrors/trunk/Insight/Testing/Code/Algorithms/itkDeformableSimplexMesh3DFilterTest.cxx

[2] error LNK2019: unresolved external symbol "public: __cdecl itk::SimplexMeshGeometry::~SimplexMeshGeometry(void)"
(??1SimplexMeshGeometry@itk@@QEAA@XZ) referenced in function "protected:
virtual __cdecl itk::SimplexMesh<double,3,class itk::DefaultDynamicMeshTraits&lt;double,3,3,double,double,double>
>::~SimplexMesh<double,3,class
itk::DefaultDynamicMeshTraits&lt;double,3,3,double,double,double> >(void)"
(??1?$SimplexMesh@N$02V?$DefaultDynamicMeshTraits@N$02$02NNN@itk@@@itk@@MEAA@XZ)
D:\Dropbox\Slicer\dev\CLI\DeformableMesh460\DeformableSimplexMesh\DeformableSimplexMesh.obj
DeformableSimplexMeshLib

[3]
https://github.com/SlicerProstate/SlicerProstate/blob/master/SegmentationSmoothing/SegmentationSmoothing.cxx



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