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[SCIRUN-USERS] Re: Help with Meshing using Biomesh3D

Chronological Thread 
  • From: Jess Tate <>
  • To: Adrienne Madison <>
  • Cc:
  • Subject: [SCIRUN-USERS] Re: Help with Meshing using Biomesh3D
  • Date: Tue, 23 Apr 2013 11:53:23 -0600

Hi Adrienne,

Depending on the segmentation resolution, number of materials, and the nature of the geometry,  BioMesh can take quite a while to run stage 7 (very large complicated meshes can take months).  We realize that this is a short coming in the software, but the upside is that it is likely still working.  It might be worth while to use a coarser version of your segmentation to allow you to tune some parameters a bit.  You can runs a down sampled version (you can do this in Seg3D) that could run overnight to make sure that everything is OK, then use the same parameters for the larger mesh.  You can use the same trick on the individual tissues also, as they complete much faster than multi material segmentations.  

As for your second mesh, it is a bit tricky to figure out what is going on here without more information.  It is likely that there is a failure in a previous stage that isn't completely crashing but giving garbage.  Make sure that you are using separate output directories in the model_config file.  It could also help to run the interactive mode to check the output of each of the stages (use the flag -id just display the outputs without running the calculation).


On Apr 23, 2013, at 8:38 AM, Adrienne Madison <> wrote:

Good Morning,

I am attempting to use the Biomesh3D module to create a FEM ready mesh for two geometries: a. Normal canine brain and b. Abnormal canine brain.  The geometries were extracted/segmented from MRI files using the Seg3D software.  The linux compatibile SCIRun (BioMesh3D) is installed on 2 computers here in the UGA Biophotonics Lab where I am a PhD candidate.

In the case of the normal brain geometry, Biomesh3D has been running upwards of 4 weeks. It has been in Stage 7 for over 2 weeks now.  I know that this model is relatively complicated, but is acceptable? 

As for the abnormal brain geometry, it completes within a few days, however, the files generated from stage 8 contain errors when opened in SCIRUN.  The message is that there is more than one material inside of an element. This geometry has tumor tissue within the normal brain tissue and after several adjustments of the max_sizing field within the file we still get the same outcome. 

Any assistance you can provide regarding these issues are greatly appreciated.  If needed I can submit the original .nrrd files from Seg3D and a copy of the output text as each stage of BioMesh3D is executed.  I look forward to your response!
Adrienne Madison
CURO Graduate Engineering Fellow
604 Driftmier Engineering Center
Athens, GA 30602

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