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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, a 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
 % or you can use the verbose form:
 % [node,elem,face]=vol2mesh(mydata>0.5,1:size(mydata,1),1:size(mydata,2),...
                           1:size(mydata,3), 5, 100, 1,'cgalsurf');
 % be careful, the last column of face is a label, should not be used for plotting, same for elem

Needless to say, the first line loads the data to your current session. The second line calls an iso2mesh function, 'v2m', 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.
  • elem: the tetrahedral element info, with a dimension of NE x 4; 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,;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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