Semiautomated segmentation of hepatocellular carcinoma tumors with MRI using convolutional neural networks

Daniela Said, Guillermo Carbonell, Daniel Stocker, Stefanie Hectors, Naik Vietti-Violi, Octavia Bane, Xing Chin, Myron Schwartz, Parissa Tabrizian, Sara Lewis, Hayit Greenspan, Simon Jégou, Jean Baptiste Schiratti, Paul Jehanno, Bachir Taouli*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Objective: To assess the performance of convolutional neural networks (CNNs) for semiautomated segmentation of hepatocellular carcinoma (HCC) tumors on MRI. Methods: This retrospective single-center study included 292 patients (237 M/55F, mean age 61 years) with pathologically confirmed HCC between 08/2015 and 06/2019 and who underwent MRI before surgery. The dataset was randomly divided into training (n = 195), validation (n = 66), and test sets (n = 31). Volumes of interest (VOIs) were manually placed on index lesions by 3 independent radiologists on different sequences (T2-weighted imaging [WI], T1WI pre-and post-contrast on arterial [AP], portal venous [PVP], delayed [DP, 3 min post-contrast] and hepatobiliary phases [HBP, when using gadoxetate], and diffusion-weighted imaging [DWI]). Manual segmentation was used as ground truth to train and validate a CNN-based pipeline. For semiautomated segmentation of tumors, we selected a random pixel inside the VOI, and the CNN provided two outputs: single slice and volumetric outputs. Segmentation performance and inter-observer agreement were analyzed using the 3D Dice similarity coefficient (DSC). Results: A total of 261 HCCs were segmented on the training/validation sets, and 31 on the test set. The median lesion size was 3.0 cm (IQR 2.0–5.2 cm). Mean DSC (test set) varied depending on the MRI sequence with a range between 0.442 (ADC) and 0.778 (high b-value DWI) for single-slice segmentation; and between 0.305 (ADC) and 0.667 (T1WI pre) for volumetric-segmentation. Comparison between the two models showed better performance in single-slice segmentation, with statistical significance on T2WI, T1WI-PVP, DWI, and ADC. Inter-observer reproducibility of segmentation analysis showed a mean DSC of 0.71 in lesions between 1 and 2 cm, 0.85 in lesions between 2 and 5 cm, and 0.82 in lesions > 5 cm. Conclusion: CNN models have fair to good performance for semiautomated HCC segmentation, depending on the sequence and tumor size, with better performance for the single-slice approach. Refinement of volumetric approaches is needed in future studies. Key Points: • Semiautomated single-slice and volumetric segmentation using convolutional neural networks (CNNs) models provided fair to good performance for hepatocellular carcinoma segmentation on MRI. • CNN models’ performance for HCC segmentation accuracy depends on the MRI sequence and tumor size, with the best results on diffusion-weighted imaging and T1-weighted imaging pre-contrast, and for larger lesions.

Original languageEnglish
Pages (from-to)6020-6032
Number of pages13
JournalEuropean Radiology
Issue number9
StatePublished - Sep 2023
Externally publishedYes


FundersFunder number
Owkin Inc.


    • Artificial intelligence
    • Carcinoma, hepatocellular
    • Deep learning
    • Magnetic resonance imaging
    • Neural networks, computer


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