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

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.