Automatic segmentation of femoral tumors by nnU-net

Oren Rachmil, Moran Artzi, Moshe Iluz, Ido Druckmann, Zohar Yosibash*, Amir Sternheim

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Background: Metastatic femoral tumors may lead to pathological fractures during daily activities. A CT-based finite element analysis of a patient's femurs was shown to assist orthopedic surgeons in making informed decisions about the risk of fracture and the need for a prophylactic fixation. Improving the accuracy of such analyses ruqires an automatic and accurate segmentation of the tumors and their automatic inclusion in the finite element model. We present herein a deep learning algorithm (nnU-Net) to automatically segment lytic tumors within the femur. Method: A dataset consisting of fifty CT scans of patients with manually annotated femoral tumors was created. Forty of them, chosen randomly, were used for training the nnU-Net, while the remaining ten CT scans were used for testing. The deep learning model's performance was compared to two experienced radiologists. Findings: The proposed algorithm outperformed the current state-of-the-art solutions, achieving dice similarity scores of 0.67 and 0.68 on the test data when compared to two experienced radiologists, while the dice similarity score for inter-individual variability between the radiologists was 0.73. Interpretation: The automatic algorithm may segment lytic femoral tumors in CT scans as accurately as experienced radiologists with similar dice similarity scores. The influence of the realistic tumors inclusion in an autonomous finite element algorithm is presented in (Rachmil et al., "The Influence of Femoral Lytic Tumors Segmentation on Autonomous Finite Element Analyses", Clinical Biomechanics, 112, paper 106192, (2024)).

Original languageEnglish
Article number106265
JournalClinical Biomechanics
StatePublished - Jun 2024


FundersFunder number
Ministry of Science and Technology, Israel


    • Femur
    • Segmentation
    • nnU-net


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