Finite element analysis of very large bone models based on micro-CT scans

TL;DR

This paper develops a scalable, open-source finite element framework for detailed biomechanical analysis of large bone models from micro-CT scans, enabling realistic simulations at an unprecedented scale.

Contribution

It introduces a comprehensive open-source $bc$FE framework for large-scale bone modeling, integrating advanced segmentation, scalable solvers, and experimental validation.

Findings

Models with over 8x10^8 DOFs solved using moderate HPC resources.

40 μm voxel size balances accuracy and computational cost.

Coupled $bc$FE and DIC measurements for material property calibration.

Abstract

High-resolution voxel-based micro-finite element ($\mu$FE) models derived from $\mu$CT imaging enable detailed investigation of bone mechanics but remain computationally challenging at anatomically relevant scales. This study presents a comprehensive $\mu$FE framework for large-scale biomechanical analysis of an intact New Zealand White (NZW) rabbit femur, integrating advanced segmentation, scalable finite element solvers, and experimental validation using predominantly open-source libraries. Bone geometries were segmented from $\mu$CT data using the MIA clustering algorithm and converted into voxel-based $\mu$FE meshes, which were solved using the open-source MFEM library with algorithms designed for large-scale linear elasticity systems. The numerical solutions were verified by comparing with a commercial finite element solver, and by evaluating the performance of full assembly and element-by-element formulations within MFEM. Models containing over $8\times10^{8}$ DOFs were solved using moderate HPC resources, demonstrating the feasibility of anatomically realistic $\mu$FE simulations at this scale. Resolution effects were investigated by comparing models with voxel sizes of 20, 40, and 80 $\mu$m, revealing that 40 $\mu$m preserves boundary displacement and principal strain distributions with minimal bias while significantly reducing computational cost. Sensitivity analyses further showed that segmentation parameters influence the global mechanical response. Finally, $\mu$FE predictions were coupled with Digital Image Correlation measurements on an NZW rabbit femur under compression to calibrate effective bone material properties at the micron scale. The results demonstrate that large-scale, experimentally informed $\mu$FE modeling can be achieved using open-source tools, providing a robust foundation for preclinical assessment of bone mechanics and treatment-related risks.