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[SCIRUN-USERS] Help with Meshing using Biomesh3D

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  • From: Adrienne Madison <>
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  • Subject: [SCIRUN-USERS] Help with Meshing using Biomesh3D
  • Date: Tue, 23 Apr 2013 10:38:46 -0400

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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