Generating 3D Tetrahedral Meshes

You can generate 3D tetrahedral meshes from the selected classes of a multi-ROI. 3D tetrahedral meshes, which are boundary meshes filled with tetrahedrals that can fit arbitrary shaped geometries, are often used for simulation purposes such as finite element modeling and other analyzes.

The following video provides an introduction to generating 3D tetrahedral meshes.

Volume Meshing (6:13)

You also view this video and others on our YouTube channel (https://www.youtube.com/channel/UCuFl2zHcyStR2RJpMXbi6ow).

Topics Covered in the Video

The following topics are discussed in the video. Links to Help topics with further information are also provided whenever possible.

Tetrahedral elements are commonly constructed as equilateral, such as in systems with circular curvature, or they could be constructed as isosceles tetrahedra when a system has asymmetry. Tetrahedral elements could also be totally unstructured and adapted to arbitrary geometries with high accuracy. The accuracy can be much higher than a simple cubic grid applied in 3D or a square grid applied in 2D.
3D tetrahedral mesh generation in Dragonfly is implemented using NetGen/NGSolve (https://ngsolve.org/).

You can generate 3D tetrahedral meshes from the selected classes of a multi-ROI. You should note that this can be a compute-intensive task and it may take a long time to complete. In some cases, it is best to downsample the image data or multi-ROI prior to generating the mesh (see Sampling Datasets).

How to Generate a 3D Tetrahedral Mesh
  1. Select the class or classes in the multi-ROI from which you want to generate a 3D tetrahedral mesh.
  2. Right-click the multi-ROI and then choose 3D Tetrahedral Mesh Generator in the pop-up menu.
  3. Enter the required values in the Generate 3D Tetrahedral Mesh dialog, shown below.

  4. Click Generate Mesh.

    The generated mesh is added to the Data Properties and Settings panel.

  5. Do the following to view the scalar information contained within the mesh:
    • Select the mesh in the Data Properties and Settings panel.
    • Check the 'Use scalar values for LUT' option in the Scalar information box, as shown below.

    • Choose the required scalar type and/or measurement.

You can export 3D tetrahedral meshes to a number of different mesh file formats, as described in the following table, as well as in the Dragonfly Object (*ORSObject extension) file format.

3D tetrahedral mesh file formats for export
  Description Export Import
NetGen mesh (*.vol) Native file format used in Netgen, which is a finite element solver.

Note Go to https://ngsolve.org/ for information about Netgen/NGSolve.

 Yes No
Gmsh mesh (*.gmsh) Native file format of Gmsh, which is an open source 3D finite element mesh generator with a built-in CAD engine and post-processor.

Note Go to https://gmsh.info/doc/texinfo/gmsh.html#Gmsh-file-formats for information about Gmsh’s native 'MSH' file format.

 Yes No
DIFFPACK mesh (*.dff) Native file format developed by Diffpack, which is an object oriented development framework for the solution of partial differential equations.

Note Go to https://diffpack.de/ for more information about Diffpack.

 Yes No
Stereolithographic surface triangular mesh (*.stl) File format native to the stereolithography CAD software created by 3D Systems and is widely used for rapid prototyping, 3D printing, and computer-aided manufacturing.

Note In this case, the exported STL file will only describe the surface geometry of a three-dimensional object. If you need to retain the internal 3D geometry, choose the option Export > Mesh to File (see Exporting Meshes).

 Yes Yes
Virtual reality modeling language surface triangular mesh (*.wrl) WRL files are an extension of the Virtual Reality Modeling Language (VRML) format.

Note In this case, the exported WRL file will only describe the surface geometry of a three-dimensional object. If you need to retain the internal 3D geometry, choose the option Export > Mesh to File (see Exporting Meshes).

 Yes Yes
How to Export a 3D Tetrahedral Mesh
  1. Right-click the required 3D tetrahedral mesh in the Data Properties and Settings panel and then choose Export > Tetrahedral Mesh to File in the pop-up menu.
  2. Select a destination folder and file name, as well as a file format, in the Export 3D Tetrahedral Mesh to File dialog.
  3. Click the Save button.