A workflow for the creation of specimen-specific Finite Element models based on open-source software: a feasibility study

Specimen specific Finite Element (FE) models are widely used in biomechanics to support personalised analysis and clinical decision making. However, the high licensing costs of commercial software remain a major barrier to accessibility. Although several open source tools have emerged as potential alternatives, achieving a complete workflow - from Computed Tomography (CT) data to numerical simulation remains challenging. This study aimed to evaluate the feasibility of constructing specimen specific FE models using a workflow based primarily on open source software. A previously published vertebral body FE study was reproduced to validate the proposed methodology. CT images of a porcine cervical vertebral body were segmented in 3D Slicer, refined in MeshMixer, and converted to a solid geometry using FreeCAD. A finite element mesh was generated in Ansys due to file format dependencies in the BoneMat open source material mapping software. Material properties were assigned based on Hounsfield Units and a densitometric calibration curve. Boundary conditions replicating the reference study were applied, and numerical analyses were performed. The resulting model reproduced the reference geometry, material distribution, and mechanical response with differences of 6% in volume, 7.89% in average Young’s modulus, and 6.09% in stiffness, with no statistically significant difference between load–displacement curves (p = 0.38). The main limitation identified was the lack of full compatibility among open source tools, particularly for material mapping and FE solving. Despite this, the study demonstrates that reliable specimen specific FE models can be constructed using a predominantly open source workflow, substantially reducing cost and improving accessibility for researchers.