Automated segmentation of knee articular cartilage: Joint deep and hand-crafted learning-based framework using diffeomorphic mapping

Somayeh Ebrahimkhani, Anuja Dharmaratne, Mohamed Hisham Jaward, Yuanyuan Wang, Flavia M. Cicuttini

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)


Segmentation of knee articular cartilage tissue (ACT) from 3D magnetic resonance images (MRIs) is a fundamental task in assessing knee osteoarthritis (KOA). However, automated ACT segmentation of knee cartilage is complicated by (1) the variability of pathological structures in terms of shape, size, spatial resolution and (2) the uncertainties in delineating inter- and intra-cartilage boundaries (possibly touching inter-cartilage surfaces, intensity inhomogeneity, cartilage loss due to disease progression). To address these problems, we propose a novel joint deep and hand-crafted learning-based (JD-HCl) framework. The fully automated segmentation pipeline is a combination of three main steps: 3D convolutional neural networks (CNNs), diffeomorphic mapping, and a conventional hand-crafted feature-based classification model. Firstly, the initial segmentation of knee ACT was drawn from preprocessed knee MRIs using 3D U-Net. Secondly, the spatial alignment in the image domain was carried out using diffeomorphic image registration derived from an estimate of the anatomical correspondences between the subjects and population-specific template. Finally, a tissue-specific hand-crafted feature set was extracted from the spatially aligned pre-segmented ACT region and combined with the semantic context priors obtained from 3D CNN model to develop the second-stage learning model. The proposed method was evaluated with two publicly available Osteoarthritis Initiative (OAI) datasets and one in-house MRI sequences from the Alfred hospital, Melbourne, Australia. The proposed JD-HCl framework produced strong Dice similarity coefficient (DSC), ranging between 97.4% and 98.5% (95% confidence interval) for all cartilage compartments at baseline to 97.2% and 98.5% (the 1-year follow-up) for OAI(-Imorphics) dataset, and 89.3% and 94.6% for OAI-ZIB validation dataset, respectively. Average correlations of cartilage volumes between manual and automatic segmentations were 0.9 and 0.83 for OAI-ZIB dataset, respectively, and 0.975, 0.995, and 0.99 for OAI(-Imorphics) validation datasets, respectively. In longitudinal studies, accurate segmentation of knee ACT using the proposed method produces reproducible cartilage volume, thickness measurements valuable for the study of KOA progression.

Original languageEnglish
Pages (from-to)36-55
Number of pages20
Publication statusPublished - 7 Jan 2022


  • Convolutional neural networks (CNNs)
  • Diffeomorphic mapping
  • Knee articular cartilage segmentation
  • Magnetic resonance imaging (MRI)
  • Osteoarthritis (OA)

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