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,

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?

[image] Van_Sy: I want to do this file in a Finite Element Sofware 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! Crayon

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.

This is a useful tool with a source code.

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.

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, Crayon

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.

Dear Andras, I am trying to convert .vtk file into inp file using meshio. the vtk file is not read by meshio. it gives error assert section == “FIELD”, “Unknown section ‘{}’.”.format(section) AssertionError: Unknown section ’ how to resolve this error. please help.

Meshio does not support binary .vtk files. You can save ascii .vtk file by checking “Show options” and unchecking “Compress” in Save data dialog. This worked for me in the Python interactor of a recent Preview Release: pip_install('meshio') import meshio mesh = meshio.read(r"c:\tmp\Model.vtk") meshio.write(r"c:\tmp\Model.inp", mesh)

Yes after unchecking compress in options it worked. thanks Andras

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

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

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