Convert a surface mesh to a volumetric mesh in 3D Slicer

(Van Sy) #1

Hello everyone,
When I use 3D SLICER, I only have a surface mesh in here. But, I want to do this file in a Finite Element Sofware, I need a volumetric mesh.
Can you tell me how to convert a surface mesh to a volumetric mesh in 3DSLICER?
Thank you so much,
Van Sy,

(Andras Lasso) #2

You can use the recently added SegmentMesher extension ( to segments (surface meshes or labelmaps) to volumetric meshes that are suitable for FEM analysis. The extension’s packaging is not fully worked out yet, so you may need to install the mesher software (Cleaver2 and/or Tetgen) and set it in the extension manually. What operating system do you use?

(Van Sy) #3

Dear Mr. Andras,
I will use Ansys Software. Thank you for your information, I will try to use these tools, but I think that it is very useful if you make a video to teach everyone “how to use these tools to convert to a volumetric mesh from a surface mesh”. I think that this topic is very powerful.

(saima safdar) #5

Hi Andras,
When I save the results of segment mesher. I see .vtk file. when I open it it dont show me exact volumetric mesh which segment mesher generated.

Is there a specific way to save the files.

I think it is volumetric mesh.

(saima safdar) #6

Dear Andras,
I used segment mesher. It is generating surface mesh instead of volumetric mesh. I used segment editor for segmenting tumor and brain. then I switched to segment mesher. It always generate surface mesh. I opened the *.vtk file of the generated model into paraview but dont see a volumetric mesh.

Please see the screen shot.

Does segmentmesher do not produce volumetric mesh? if yes what am I doing wrong? would you please correct me?

Create a volumetric mesh
(Andras Lasso) #7

Segment mesher extension generates a volumetric mesh (unstructured grid containing tetrahedron and maybe also wedge cells). Why do you think the mesh is not a volumetric mesh?

(xx) #9

Hi Van Sy,
I think I have met with the similar problem. I want to segment a structure (breast tumor) from MR image and then import the model to Ansys Software for finite element analysis. But I found the result of segmentation was surface mesh, which can’t be imported to ICEM for meshing (it needs to be geometry?). I wonder if you were meshing directly in Slicer (using Segment Mesher?) and then importing the volumetric mesh to Ansys just for subsequent analysis. Whatif I want to get a “geometry” from surface mesh in Slicer?
Hope for some advice, thank you!

(Andras Lasso) #10

ICEM can import surface meshes (STL files) - see for example this old forum topic. Segment Mesher can generate tetrahedral meshes that you can save in VTK unstructured grid (.vtu) file format. You may need a mesh conversion utility to convert it to a file format that can be read by your FEM software.

( #11

This is a useful tool with a source code.

(Andras Lasso) #12

The issue is not that we wouldn’t have volumetric mesh generators in Slicer. We can generate volumetric meshes in Slicer using Cleaver2 or Tetgen via Segment Mesher extension. The issue is that the output file format (vtk unstructured grid) cannot be directly read by the commercial solvers or pre-processors.

The robust_hex_dominant_meshing mesh generator referenced above does not solve this issue, as it generates files in the same VTK file format (.vtu), medit (.mesh) file format, or a custom internal (.hybrid) file format. I think ICEM cannot read any of these.

Solution can be to use mesh converter tools, such as meshio, which can read VTK volumetric mesh from .vtu file and can write it as an Ansys .msh file.

(xx) #13

Thank you all for the discussion. ICEM can indeed import mesh from unstructured grid, but in fact failed to import from vtu or vtk format. Meshio can successfully convert .vtu file to .msh file which can read by the ICEM. Another way I tried was to convert the surface mesh created by Slicer segmentation module to solid geometry in Solidworks (IGES format). One more question please, I wonder if the output results of Slicer segmentation module just contain two types (surface mesh named model and labelmap)?

Best regards,

(Csaba Pinter) #14

Yes the most typical exported formats from segmentation are closed surface (model node) and binary labelmap. You can also export to planar contours and fractional labelmap with the current version.

Maybe we could add segmentation converter rules that use Cleaver2 / Tetgen and can generate volumetric mesh within the segmentation.