How to smooth surface mesh of volume mesh from 3d image

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How to smooth surface mesh of volume mesh from 3d image

Kim Donghyeon

Hi, I have a question about CGAL volume meshing.

 

Im working on generating head mesh from 3d medical image (already segemented).

 

It is exactly same as brain mesh picture on 3D Mesh Generation user manual. (https://doc.cgal.org/latest/Mesh_3/index.html)

 

My problem is, I could generate volume mesh, but thr surface of each label is very rough (not smooth)

 

The resolution of segmented image is 256 * 256 * 256 (1mm * 1mm * 1mm). And also, I compared the result of Cleaver2 mesher and cgal mesher.

 

I understand it could have different result. But cgal have rough surface mesh compared with the result of cleaver2.

 

I think I missused volume mesh paramemter.

 

(my input data is: https://drive.google.com/file/d/1DUt-gSZ2uM8Rzv_9tfb80aWOmPLXbPl0/view?usp=sharing  )

 

My code is based on Mesh_3/mesh_3D_image_variable_size.cpp and used

 

           double facet_angle = 30;

           double facet_size = 2;

           double facet_distance = 2;

           Sizing_field cell_radius_edge_ratio(1.5);

 

To solve it, I already changed facet_size from 0.00001 to 2, but it does not affect the result (I did same value on facet_distance).

 

Is it a normal situiation? and could you give an advice for me?

 

Also I just want to know the detailed parameter of the brain mesh which is on the top of 3D Mesh Generation document and chest mesh which figure number is 54.22

 

Thank you

Kim

 

 

김동현 Donghyeon Kim
Co-Founder / Chief Technology Officer (CTO)
NEUROPHET

Mobile : +82-10-9361-3781
E-mail : [hidden email]

Disclaimer: This message contains privileged confidential information which is not to be disclosed. If you are not the intended recipient of this message please contact the sender and destroy this message as well as all existing copies and attachments.

 


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Re: How to smooth surface mesh of volume mesh from 3d image

Laurent Rineau (CGAL/GeometryFactory)
Le Tuesday, February 20, 2018 10:53:42 AM CET Kim Donghyeon a écrit :
> Hi, I have a question about CGAL volume meshing.
>
> I’m working on generating head mesh from 3d medical image (already
> segemented).
 
> It is exactly same as brain mesh picture on 3D Mesh Generation user manual.
> (https://doc.cgal.org/latest/Mesh_3/index.html)
 
> My problem is, I could generate volume mesh, but thr surface of each label
> is very rough (not smooth)
 
> The resolution of segmented image is 256 * 256 * 256 (1mm * 1mm * 1mm). And
> also, I compared the result of Cleaver2 mesher and cgal mesher.
 
> I understand it could have different result. But cgal have rough surface
> mesh compared with the result of cleaver2.
 
> I think I missused volume mesh paramemter.
>
> (my input data is:
> https://drive.google.com/file/d/1DUt-gSZ2uM8Rzv_9tfb80aWOmPLXbPl0/view?usp
> =sharing  )
 
> My code is based on “Mesh_3/mesh_3D_image_variable_size.cpp” and used
>
>            double facet_angle = 30;
>            double facet_size = 2;
>            double facet_distance = 2;
>            Sizing_field cell_radius_edge_ratio(1.5);
>
> To solve it, I already changed facet_size from 0.00001 to 2, but it does
> not affect the result (I did same value on facet_distance).
 
> Is it a normal situiation? and could you give an advice for me?

Hi Kim,

In the example code, replace the line:

    Mesh_domain domain(image);

with

    Mesh_domain domain(image, 1e-6);


The default value for that second parameter is 1e-3, and that is too low for
precise images like the one you use. That parameter sets the precision of the
bissection algorithm used to compute intersections with the implicit surfaces
of the image and query segments. I think the image

> Also I just want to know the detailed parameter of the brain mesh which is
> on the top of 3D Mesh Generation document and chest mesh which figure
> number is 54.22

That image was created using the CGAL 3D demo (the code is in demo/
Polyhedron/), and I think the Mesh_3 uses 1e-6 for that parameter.

--
Laurent Rineau, PhD
R&D Engineer at GeometryFactory           http://www.geometryfactory.com/
Release Manager of the CGAL Project       http://www.cgal.org/




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RE: How to smooth surface mesh of volume mesh from 3d image

Kim Donghyeon

Thank you for reply.

 

Based on your comment (setting accuracy e-6) I tried to make mesh.

 

Following is the result.

 

https://docs.google.com/presentation/d/1dMXqGMFpqIv0UwJr3Fd7N-hZAKEsy0ukpbTa-GdRpQI/edit?usp=sharing

 

However, still surface is not smooth. I reslly want to make a mesh like Figure 54.1 (https://doc.cgal.org/latest/Mesh_3/)

 

Its surface is enough to smooth.

 

Should I set an additional parameter?

 

Thank you

Kim.

 

김동현 Donghyeon Kim
Co-Founder / Chief Technology Officer (CTO)
NEUROPHET

Mobile : +82-10-9361-3781
E-mail : [hidden email]

Disclaimer: This message contains privileged confidential information which is not to be disclosed. If you are not the intended recipient of this message please contact the sender and destroy this message as well as all existing copies and attachments.

 


보낸 사람: Laurent Rineau (CGAL/GeometryFactory) <[hidden email]>
보낸 날짜: Wednesday, February 21, 2018 12:00:37 AM
받는 사람: [hidden email]
참조: Kim Donghyeon
제목: Re: [cgal-discuss] How to smooth surface mesh of volume mesh from 3d image
 
Le Tuesday, February 20, 2018 10:53:42 AM CET Kim Donghyeon a écrit :
> Hi, I have a question about CGAL volume meshing.
>
> I’m working on generating head mesh from 3d medical image (already
> segemented).
 
> It is exactly same as brain mesh picture on 3D Mesh Generation user manual.
> (https://doc.cgal.org/latest/Mesh_3/index.html)
 
> My problem is, I could generate volume mesh, but thr surface of each label
> is very rough (not smooth)
 
> The resolution of segmented image is 256 * 256 * 256 (1mm * 1mm * 1mm). And
> also, I compared the result of Cleaver2 mesher and cgal mesher.
 
> I understand it could have different result. But cgal have rough surface
> mesh compared with the result of cleaver2.
 
> I think I missused volume mesh paramemter.
>
> (my input data is:
> https://drive.google.com/file/d/1DUt-gSZ2uM8Rzv_9tfb80aWOmPLXbPl0/view?usp
> =sharing  )
 
> My code is based on “Mesh_3/mesh_3D_image_variable_size.cpp” and used
>
>            double facet_angle = 30;
>            double facet_size = 2;
>            double facet_distance = 2;
>            Sizing_field cell_radius_edge_ratio(1.5);
>
> To solve it, I already changed facet_size from 0.00001 to 2, but it does
> not affect the result (I did same value on facet_distance).
 
> Is it a normal situiation? and could you give an advice for me?

Hi Kim,

In the example code, replace the line:

    Mesh_domain domain(image);

with

    Mesh_domain domain(image, 1e-6);


The default value for that second parameter is 1e-3, and that is too low for
precise images like the one you use. That parameter sets the precision of the
bissection algorithm used to compute intersections with the implicit surfaces
of the image and query segments. I think the image

> Also I just want to know the detailed parameter of the brain mesh which is
> on the top of 3D Mesh Generation document and chest mesh which figure
> number is 54.22

That image was created using the CGAL 3D demo (the code is in demo/
Polyhedron/), and I think the Mesh_3 uses 1e-6 for that parameter.

--
Laurent Rineau, PhD
R&D Engineer at GeometryFactory           http://www.geometryfactory.com/
Release Manager of the CGAL Project       http://www.cgal.org/