Abstract:
This work represents an investigation and demonstration of a strategy, using a pipeline
of open source software for computational biomechanics. The purpose is to extract 3D
models from MRI data and perform Finite Element Analysis and ensure faithfulness
in open simulation. The methodology considers four robust open-source workbenches
including 3D Slicer (for segmentation), Blender (for cleaning and fixing STL models and
setting up physical boundary conditions), Salome-Meca (for Finite Element Analysis
and Post-Processing) and Paravis (for Post Processing and Visualization). The model
for this study consisted of a vertebra and an inter-vertebral disk from human spine.
Raw model was extracted from 3D slicer. Then it was pre-processed in Blender and
finally finite element analysis was performed in Salome-Meca. While conceiving the
initiative of free pipeline for this particular study in computational biomechanics, it was
assured to guarantee the full control of the implemented functions. Not only this, the
parameterization and interchangeability between the workbenches was also entrusted.
Fixing serious mesh problems like singularity, free and intersecting elements is special
contribution of this study using open source workbench. Generation of contact surfaces
and categorization in groups, pivotal for assemblage later in Code_Aster, with a Blender
script was also implemented which is very similar to how they are done in licensed
workbenches for FEM. Another major highlight of this work is a novel strategy to
separate a vertebra from the spinal column using 3D slicer. The results from Code_Aster
were cross validated with with commercial computer solvers. In conclusion, apart from
free software benefits, it is a recommended solution for all professionals in the field of
computational biomechanics and relative researches where mathematical modeling is an
emerging field and ability to customize the software shouldn’t be limited.
