BioMedical STL Repair, Any Suggestions?
 

Hey, all, thanks for reading this post.

I have a problem with STL file repair. I work with biomedical applications, so repairing STL files is a mess, especially when it comes to Brain and Spinal CSF representations, where you have 50K to 200K surface elements in a complex geometry.

I use ICEM CFD, and although the autofixing tool is great, I can't really use it. Every time I use it, it considers some of the complex geometry bad elements and tries to "fix" it, leaving me with a STL file I can no longer use (because its no longer physiologically consistent). When I try to mesh it right from the go (right after registration from MRI images), I get hundreds of created elements. Should I just merge these volumes, and be done with it?

Thanks again for your advice, this forum is exactly what I needed for CFD analysis.

Check the geometry...
 

I usually start with the surface and check it out to see how bad it is...

Use the top menus; Edit => Facets to Mesh. We just need it as mesh to run the diagnostics. Then run the Edit Mesh Tab Diagnostic to check for single edges (holes or tabs), multiple edges, triangle boxes, etc. Put each of these into a subset as you go thru. Then investigate each subset (under the mesh branch, turn on the subset and turn off all the other mesh types).

For each subset, right click and add layers (twice). Then look at what you have on the screen. Do you have a lot of holes? Many Triangle boxes? If you don't have too many problems, you can fix them manually (not the autofixing tool). Even a hundred problems can be fixed pretty quickly (you get faster with practice), but if you have thousands, you should at least adjust your expectations or perhaps consider the effort required to get better data...

When you are done editing the mesh, you can convert it back to facets (replace the geometry and then delete the mesh).

Some Meshing tips...
 

Are you meshing around the brain or inside the brain or both?

If around the brain and it is fairly water tight... You can put a material point in the space around the brain and run octree to get a single volume...

If you are meshing inside the brain, and want to keep all the surfaces (even those surfaces that have the same volume material on both sides), you will need to go to Mesh (tab)=> Params by Parts and turn on the Internal Wall option for the Brain Part. You would need a material point inside each closed volume of the brain...

If you have a lot of triangle boxes and don't fix them, each one would end up creating its own closed volume... If you create even 1 material point, all those triangle boxes will be empty (fluid deleted by the flood fill). If you want each of those volumes filled with fluid, you must not create any material points while you are meshing... You can create them after, such as 1 for the area in the brain an one for outside, then Edit Mesh => Repair => FloodFill. Then Right click on the Brain Material in the tree, Add to Part. Then use the Selection Toolbar to Select elements By Part. Select all the "CREATED_MATERIAL" Parts and apply.

Start with these two posts and let me know where you are...