Reducing Annotation Burden for Femoral Cartilage Segmentation in Knee MRI via Cross-Sequence Transfer Learning
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| Main Authors: | , , , , , , , , , |
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| Format: | Preprint |
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2026
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| author | Chiumento, Francesco Crimi, Gianluigi Moretta, Elisa Milieri, Rocco Bazzocchi, Alberto Vara, Giulio Fabbro, Giacomo Dal Zaffagnini, Stefano Taddei, Fulvia Bonaretti, Serena |
| author_facet | Chiumento, Francesco Crimi, Gianluigi Moretta, Elisa Milieri, Rocco Bazzocchi, Alberto Vara, Giulio Fabbro, Giacomo Dal Zaffagnini, Stefano Taddei, Fulvia Bonaretti, Serena |
| contents | Purpose: To develop and evaluate cross-sequence transfer learning for automatic femoral cartilage segmentation, testing bidirectional transfer between dual-echo steady-state (DESS) and sagittal proton density-weighted 3D fast spin-echo (Cube) sequences. Materials and Methods: We optimized a modified 2D U-Net on 507 DESS images from the Osteoarthritis Initiative (OAI). We then established same-sequence baselines using subject-level cross-validation on a subset of 44 OAI DESS images and 44 Cube images acquired at the Istituto Ortopedico Rizzoli, Bologna, Italy. Each subset included 22 non-lesioned and 22 lesioned subjects. Finally, we performed transfer learning across sequences by fine-tuning the pretrained models on the target sequence with increasing training set sizes to study convergence, while keeping validation and test sets fixed. Segmentations were evaluated using Dice similarity coefficient (DSC) and average surface distance (ASD). Lesion effects were assessed with two-sided Mann-Whitney U tests with Bonferroni correction. Results: Same-sequence training yielded higher accuracy on DESS than Cube (DSC, $0.900$ vs $0.830$; $P < .001$). Cube-to-DESS transfer matched DESS performance (DSC, $0.903 \pm 0.032$ vs $0.900 \pm 0.027$), reaching a performance plateau at 9 training subjects. DESS-to-Cube yielded a lower combined DSC ($0.802 \pm 0.049$ vs $0.830 \pm 0.042$), reaching a plateau at 24 training subjects. Lesions did not affect DESS ($P \ge .39$) but reduced Cube accuracy (DSC, $0.805$ vs $0.856$; $P < .001$). Conclusion: Transfer learning across sequences can substantially reduce target-sequence annotation requirements for femoral cartilage segmentation, but performance is direction- and sequence-dependent, and the effects of lesions on segmentation may vary across MRI sequences. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2605_09067 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | Reducing Annotation Burden for Femoral Cartilage Segmentation in Knee MRI via Cross-Sequence Transfer Learning Chiumento, Francesco Crimi, Gianluigi Moretta, Elisa Milieri, Rocco Bazzocchi, Alberto Vara, Giulio Fabbro, Giacomo Dal Zaffagnini, Stefano Taddei, Fulvia Bonaretti, Serena Computer Vision and Pattern Recognition Purpose: To develop and evaluate cross-sequence transfer learning for automatic femoral cartilage segmentation, testing bidirectional transfer between dual-echo steady-state (DESS) and sagittal proton density-weighted 3D fast spin-echo (Cube) sequences. Materials and Methods: We optimized a modified 2D U-Net on 507 DESS images from the Osteoarthritis Initiative (OAI). We then established same-sequence baselines using subject-level cross-validation on a subset of 44 OAI DESS images and 44 Cube images acquired at the Istituto Ortopedico Rizzoli, Bologna, Italy. Each subset included 22 non-lesioned and 22 lesioned subjects. Finally, we performed transfer learning across sequences by fine-tuning the pretrained models on the target sequence with increasing training set sizes to study convergence, while keeping validation and test sets fixed. Segmentations were evaluated using Dice similarity coefficient (DSC) and average surface distance (ASD). Lesion effects were assessed with two-sided Mann-Whitney U tests with Bonferroni correction. Results: Same-sequence training yielded higher accuracy on DESS than Cube (DSC, $0.900$ vs $0.830$; $P < .001$). Cube-to-DESS transfer matched DESS performance (DSC, $0.903 \pm 0.032$ vs $0.900 \pm 0.027$), reaching a performance plateau at 9 training subjects. DESS-to-Cube yielded a lower combined DSC ($0.802 \pm 0.049$ vs $0.830 \pm 0.042$), reaching a plateau at 24 training subjects. Lesions did not affect DESS ($P \ge .39$) but reduced Cube accuracy (DSC, $0.805$ vs $0.856$; $P < .001$). Conclusion: Transfer learning across sequences can substantially reduce target-sequence annotation requirements for femoral cartilage segmentation, but performance is direction- and sequence-dependent, and the effects of lesions on segmentation may vary across MRI sequences. |
| title | Reducing Annotation Burden for Femoral Cartilage Segmentation in Knee MRI via Cross-Sequence Transfer Learning |
| topic | Computer Vision and Pattern Recognition |
| url | https://arxiv.org/abs/2605.09067 |