Getting Started with iso2mesh

Although iso2mesh provides a rich collection of mesh-related functions, the core functionality, i.e. creating volumetric meshes from surfaces or binary image stacks, is very straightforward to use. A minimum step to perform such task only requires about 3 to 5 lines of matlab code. You can find a list of examples under the "sample" directory. In this page, we summarize the overall work-flow of this toolbox.

To outline a simple meshing session, let's assume you have a 3D image array, named "mydata", saved in a file called "mydata.mat". Variable mydata can be any 3D image, an MRI/CT scan or a simple binary mask produced by your own command. Here are the commands you need to produce a volumetric FEM mesh from this volume:

 load mydata.mat

Apparently, the first line loads the volumetric image data into your current session. The second line calls an iso2mesh function, 'v2m', the shortcut for vol2mesh, to construct a volumetric mesh from this data array. The first argument of v2m, "mydata", is the volumetric image you are about to mesh; the 2nd argument is the threshold value at which you define the boundary surface of the mesh; the 3rd argument, 5, defines the maximum size of the surface triangles; the last argument, 100, defines the maximum volume of the resulting tetrahedral elements. You can define a vector for the second argument, asking iso2mesh to produce multiple level-sets as the exterior or internal interfaces of the target domain. Both the 3rd and 4th arguments controls the density of the resulting mesh: the smaller the values, the more triangles on the surface and more tetrahedra in the volumetric mesh.

There are 3 outputs from v2m command:

  • node: the node coordinates for the generated volumetric mesh, with dimension of NN x 3, with each column being x, y and z, respectively; NN is the number of nodes.
  • elem: the tetrahedral element info, with a dimension of NE x 4, NE being the number of tetrahedral elements; each row represents an element, and each column are the node indices for each corner of a tetrahedron.
  • face: triangular surface element info, with a dimension of NS x 4, NS being the number of surface triangles;the first 3 columns are the node indices of each corner of the triangle, and the last column is a flag to identify its mapping to the original surface id.
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