Automated surgical planning with nnU-Net: delineation of the anatomy in hepatobiliary phase MRI

Karin A. Olthof; Matteo Fusagli; Bianca Güttner; Tiziano Natali; Bram Westerink; Stefanie Speidel; Theo J. M. Ruers; Koert F. D. Kuhlmann; Andrey Zhylka

arXiv · 2508.14133

Automated surgical planning with nnU-Net: delineation of the anatomy in hepatobiliary phase MRI

Karin A. Olthof·Matteo Fusagli·Bianca Güttner·Tiziano Natali·Bram Westerink·Stefanie Speidel·Theo J. M. Ruers·Koert F. D. Kuhlmann·Andrey Zhylka

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Abstract

Background: The aim of this study was to develop and evaluate a deep learning-based automated segmentation method for hepatic anatomy (i.e., parenchyma, tumors, portal vein, hepatic vein and biliary tree) from the hepatobiliary phase of gadoxetic acid-enhanced MRI. This method should ease the clinical workflow of preoperative planning. Methods: Manual segmentation was performed on hepatobiliary phase MRI scans from 90 consecutive patients who underwent liver surgery between January 2020 and October 2023. A deep learning network (nnU-Net v1) was trained on 72 patients with an extra focus on thin structures and topography preservation. Performance was evaluated on an 18-patient test set by comparing automated and manual segmentations using Dice similarity coefficient (DSC). Following clinical integration, 10 segmentations (assessment dataset) were generated using the network and manually refined for clinical use to quantify required adjustments using DSC. Results: In the test set, DSCs were 0.97+/-0.01 for liver parenchyma, 0.80+/-0.04 for hepatic vein, 0.79+/-0.07 for biliary tree, 0.77+/-0.17 for tumors, and 0.74+/-0.06 for portal vein. Average tumor detection rate was 76.6+/-24.1%, with a median of one false-positive per patient. The assessment dataset showed minor adjustments were required for clinical use of the 3D models, with high DSCs for parenchyma (1.00+/-0.00), portal vein (0.98+/-0.01) and hepatic vein (0.95+/-0.07). Tumor segmentation exhibited greater variability (DSC 0.80+/-0.27). During prospective clinical use, the model detected three additional tumors initially missed by radiologists. Conclusions: The proposed nnU-Net-based segmentation method enables accurate and automated delineation of hepatic anatomy. This enables 3D planning to be applied efficiently as a standard-of-care for every patient undergoing liver surgery.

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Karin A. Olthof, Matteo Fusagli, Bianca Güttner, Tiziano Natali, Bram Westerink, Stefanie Speidel, Theo J. M. Ruers, Koert F. D. Kuhlmann, Andrey Zhylka. 2025-08-19. Automated surgical planning with nnU-Net: delineation of the anatomy in hepatobiliary phase MRI. https://arxiv.org/abs/2508.14133

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