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Re: [Seg3D] [SCIRUN-USERS] Inconsistency in the volume mesh

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  • From: Jess Tate <>
  • To: Purbasha Garai <>
  • Cc:,
  • Subject: Re: [Seg3D] [SCIRUN-USERS] Inconsistency in the volume mesh
  • Date: Wed, 1 Jul 2015 11:18:42 -0600

Hi Purbasha,

Meshing thin features like this is a challenge that many software has problems with.  You could increase your resolution of your segmentation, which would take longer to compute.  Ideally, there would be many voxels between interfaces, but you should at least have 3.  If you have that low of sampling, you will have problems with the smoothing (tightening) that Biomesh does, which I think is what your problem is.  You can reduce/eliminate smoothing by lowering the mat_radii variable in the model config file (set to 0 for no smoothing).  If you increase the resolution, you can do more smoothing.

There are some other tricks that are more complicated.  If you do not have multiple regions that interface, but have concentric regions, you can split up the regions in to individual layers, run biomesh on each layer individually to create a surface for each interface, and combine them with tetgen (in scirun or gmesh).  with this method, you can smooth as much as desired, yet may not work with your data because there are multi-material interface.  

Biomesh cannot take surfaces as inputs.  However, you can add a surface into the pipeline by replacing the isosurface temp file (indicator function) in the biomesh output folder.  With multiple segmented regions, you will need to be careful to ensure that the interfaces are still valid (both tissue have the same boundary).


On Jun 18, 2015, at 10:46 AM, Purbasha Garai <> wrote:


I am using Biomesh 3D to build a model of nerve. It consists of a thin tissue layer (perineurium; around 0.06mm) around fascicle. Although, I am able to generate the tetrahedral mesh of the whole model, but there is inconsistency in the tissue layer (needs to be circular). Can you please suggest me how I can fix it? 


I have 5 components in my nerve model
( fig below: from inside to outside: fascicles, perineurium, epineurium, electrode ring, saline

I can see there is some roughness in all the layers of my model. Is there a way to smoothen out the data?

Fig: As you can see there are rough edges on the outside on the electrode component.

Is there any way to add surface mesh into the Biomesh 3D. I am using gmsh to generate the mesh, but I couldnt get the results even after running for a week.  

Thank you so much


  • Re: [Seg3D] [SCIRUN-USERS] Inconsistency in the volume mesh, Jess Tate, 07/01/2015

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