Frequently asked questions about iso2mesh
- 1. I am getting a "Two subfaces ... are found intersecting each other" error, what should I do?
- 2. After mesh generation, the surface plot looks messed up, what was wrong?
- 3. Matlab complains about imread, imclose or imfill missing
- 4. iso2mesh failed when writing files to disk
- 5. When displaying a surface produced by iso2mesh, there are many holes, how to fix this?
- 6. Subroutine meshresample returns an empty mesh, why?
- 7. Which meshing option should I choose?
- 8. How do I control mesh density in iso2mesh?
- 9. How to mesh a domain containing multiple isolated objects ?
1. I am getting a "Two subfaces ... are found intersecting each other" error, what should I do?
This is the most frequently encountered problem using this toolbox. There are three possible causes of this error:
1. the volume you are trying to mesh contains joint regions between more than 2 materials
This is most likely happening when you see the above error message. Try to plot your volume slice by slice, and pay attention to any voxels whose neighbors have more than 2 different values. If this is the case, you can only use this type of input with vol2mesh/v2m with 'cgalmesh' option as the "method" parameter
. If you use either "simplify" or "cgalsurf" (default) options, iso2mesh will fail. If for some reason you have to use these options, here are two possible temporary work-arounds:
- if there are not many junction voxels, you may want to manually edit your image and disconnect the regions that share the same boundary and make sure all the sub-regions are either completely disjointed, or completely enclosed by another.
- merge the regions that have shared boundaries, and mesh the resulting merged volume; after you get the tetrahedra, compute the centroid of each element in the merged domain (identified by their labels), and map them back to your original segmented image; determine the original region id using the voxel containing the centroids.
If you have any better suggestions to enable iso2mesh to handle this situation, please let me know.
2. you are using 'simplify' method to mesh a complex domain
There are two possible methods for volume-to-surface conversion, 'simplify' and 'cgalsurf'. The second method always returns a well-posed surface where no self-intersecting elements present; however, the 'simplify' approach does not. The default method for vol2mesh/vol2surf (v2m/v2s) is 'cgalsurf'. If you have to use 'simplify', you may have to experiment different surface densities for the surface extraction. You may lucky enough to find a working configuration, but very likely, you may not. Please use 'cgalsurf' option whenever possible.
3. your surface mesh is too coarse and intersects the enclosed surfaces
The mesh extraction will represent the region boundaries by a sheet of triangles. Near sharp edges, this representation may generate a rounded edge and does not exactly preserve the shape of the original domain. If you happen to mesh a thin layer of material, the resulting surface may intersect each other at sharp edges if your surface element is too big. Please use a small opt.radbound value to run the mesh generation again.
2. After mesh generation, the surface plot looks messed up, what was wrong?
It is very likely you incorrectly used the output variables. The output of vol2mesh or surf2mesh include elem: the tetrahedral element indices, and face: the surface triangle indices. But be careful, both of these two arrays have an additional column. The last column is a label field, indicating the origin (sub-region) of the elements. You should never use the last columns of these two arrays for plotting. To make a correct surface plot, you should use something like
and don't use the full face array as the first parameter.
If you are using iso2mesh newer than 0.9.8, you can use a function called "plotmesh" to visualize the produced surfaces and volumes. The script will attempt to recognize the extra column of "face" by using the Euler characteristics and automatically ignore it if present.
3. Matlab complains about imread, imclose or imfill missing
Under the sample/ directory, demo_vol2mesh_ex2.m requires imread
, which is a build-in function in matlab, but not in octave. You have to install octave-image
via apt-get or yum first. In example demo_vol2mesh_ex3.m, functions imclose and imfill are needed. These two functions can only be found in matlab's image processing toolbox. If you don't have this toolbox installed (of course, it is not free), you can simply pass this example. For octave, unfortunately, these functions do not exist yet, and hopefully someone can fill them in soon.
4. iso2mesh failed when writing files to disk
If you are working on a multi-user workstation, and multiple users were using iso2mesh, some temporary files may have a conflict in read/write permission under /tmp directory. If user A runs iso2mesh first, and user B will get this error, because iso2mesh fails to create the temporary files as it does not have the permissions to overwrite those files created by A. To solve this issue, please define your own temporary folder, or set your session id, you can find more info at Advanced
5. When displaying a surface produced by iso2mesh, there are many holes, how to fix this?
The node orders in the output surface mesh are random, some are oriented clockwise, some are counter-clockwise. This will make OpenGL, or OpenGL based applications, render the surface with different materials. To correct this, you can simply call
and the new surface: [newnode,newface] will have consistent orientations. Again, be careful if you are using the face output from vol2surf/v2s, it has an extra column. You only need to use the first 3 columns in the face array when making plots.
6. Subroutine meshresample returns an empty mesh, why?
When the input surface mesh contains topological defects, such as non-manifold nodes, the meshresample() subroutine will not proceed and return an empty mesh (the output message will show "0 total edges collapsed"). In this case, you need to first call meshcheckrepair() subroutine to fix your input mesh, and them pass it to meshresample. An example is shown below:
(this issue is automatically corrected in iso2mesh 0.8 or newer)
7. Which meshing option should I choose?
Iso2mesh provides 3 options for v2m and vol2mesh, namely, 'cgalmesh', 'cgalsurf' and 'simplify'. Some users may get confused which one to use. In fact, we were hoping not to put users in this situation, as iso2mesh was designed for simplicity and efficiency. Unfortunately, we haven't really found a single option that works for all of the situations, and each of the 3 options have there good and bad sides.
- cgalmesh: this is the most powerful option of all, and is potentially the ideal candidate as the default option. With 'cgalmesh', iso2mesh can easily process a binary volume and a volume with multi-region labels with good speed and robustness. It can produce both volumetric and surfaces meshes at the same time, and clearly labels the element and surfaces for each individual sub-region. However, it is not perfect. It can not extract iso-surfaces from a gray-scale image. When you want to control mesh densities near a specific isosurface (such as this case), cgalmesh option is not as flexible as the other two. In short, cgalmesh is the best choice for producing uniform-sized meshes from an arbitrary segmented volume.
- cgalsurf: cgalsurf option produces surface and volumetric meshes with a standard 2-step process as shown in the workflow. When extracting multiple isosurfaces, it will do the extraction sequentially. The strengths of cgalsurf include 1) all the extracted surfaces are guaranteed to be free of self-intersecting elements, individually, and 2) it can handle gray-scale volumes. The main issue for cgalsurf is when multiple isosurfaces overlap to each other, v2m/vol2mesh will break as the combined surface contains self-intersecting elements. In short, cgalsurf is the best option when multiple sub-regions are disconnected, or one enclosing another.
- simplify: this is as flexible as cgalsurf, but it is not as reliable. After the mesh simplification, a surface may become self-intersecting and v2m/vol2mesh will stop working. However, when you only have a dense surface to start with, this is the only option you can use.
To make it easy to remember:
- when meshing a simple binary volume, 'cgalmesh' and 'cgalsurf' are both good choices
- when meshing a segmented volumes with multiple sub-regions, use 'cgalmesh'
- when meshing a gray-scale volume, use 'cgalsurf'
- when other options fail, try 'simplify'.
8. How do I control mesh density in iso2mesh?
Iso2mesh uses two parameters to quantitatively control the
mesh density. In v2m or vol2mesh, parameter opt sets the
maximum edge length of the surface triangles (i.e.
controlling the density of the mesh on the surface),
and maxvol sets the maximum tetrahedron volume.
If you want to let the mesh be denser on the surface and
coarser inside, you can use a small opt value and a large
If you want to control the surface mesh density so that
it adapts depending on the curvature, you can do so by
defining opt as a struct, and set the opt.radbound and
opt.distbound values. You can find examples from
this presentation (slide 15).
This example can also be accessed from iso2mesh/sample/demo_helloworld.m
9. How to mesh a domain containing multiple isolated objects ?
This is a known issue with the CGAL surface mesher and 3D mesher. A bug report
has been filed here,
but it was not known if any fix has been applied upstream.
For v2m/v2s with a 'cgalmesh' option, a simple work-around is to remove
zero-voxels by adding 1 to the 3D image. Then cgalmesher should be able
to recover all inclusions, along with the background. You can then
remove the background by checking the domain ID. For example:
[no,el]=v2m(uint8(img+1), , opt, maxvol, 'cgalmesh');
If the target domain is a binary image, there is another work-around:
% Author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
fprintf(1,'meshing region #%d ...\n',regionid);
% merge the resulting mesh with other regions
This function only works in Matlab because function bwlabeln
is not available in Octave.