Femurs segmentation by machine learning from CT scans combined with autonomous finite elements in orthopedic and endocrinology applications

Zohar Yosibash*, Yekutiel Katz, Trabelsi Nir, Amir Sternheim

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Efficient, accurate and reliable segmentation of femurs from CT-scans is of major importance for patient-specific autonomous finite element analysis (AFE) to determine bone's stiffness and strength. We present a fully automated segmentation algorithm for whole and partial femurs with or without tumors, and clinical applications of the AFE [1] in clinical practice. The segmentation is based on an U-Net convolutional neural network, resulting a 3D mask representing the desired femur in a CT scan. It is robust, independent of the scanning parameters such as slice spacing, pixel size, scanner manufacturer or the femoral length available in the scan. The U-Net was trained on 178 manually segmented femurs (23,721 images) and tested on 43. The performance evaluation resulted in a Dice similarity score (DSC) of 0.9924, intersection over union (IoU) of 0.9849, Hausdorff distance of 4.3315 mm and symmetric average surface distance (ASD) of 0.1326 mm. The algorithm is competitive with the best state-of-the-art femoral segmentation methodologies available. Based on the segmentation an automatic p-FE mesh is generated and physiological boundary conditions representing sidewise falls or stance are being applied automatically to improve the performance of the AFE described in [1]. New examples of the usage of the AFE in endocrinology and orthopedic oncology demonstrate this disruptive technology in actual clinical practice. We present the use of AFE for predicting hip fracture risk in the elderly population due to a sidewise fall and the identification of patients who require a prophylactic surgery due to metastatic tumors in their femurs.

Original languageEnglish
Pages (from-to)16-27
Number of pages12
JournalComputers and Mathematics with Applications
StatePublished - 15 Dec 2023


FundersFunder number
Ministry of Science and Technology, Israel
Israel Innovation Authority


    • Autonomous finite element method
    • Deep learning
    • Femur
    • Segmentation
    • U-Net


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