Abdomen CT multi‐organ segmentation using token‐based MLP‐Mixer
Authors: Pan Shaoyan , Chang Chih‐Wei , Wang Tonghe , Wynne Jacob , Hu Mingzhe , Lei Yang , Liu Tian , Patel Pretesh , Roper Justin , Yang Xiaofeng 
Published: December 2022

Background

Manual contouring is very labor‐intensive, time‐consuming, and subject to intra‐ and inter‐observer variability. An automated deep learning approach to fast and accurate contouring and segmentation is desirable during radiotherapy treatment planning.

Purpose

This work investigates an efficient deep‐learning‐based segmentation algorithm in abdomen computed tomography (CT) to facilitate radiation treatment planning.

Methods

In this work, we propose a novel deep‐learning model utilizing U‐shaped multi‐layer perceptron mixer (MLP‐Mixer) and convolutional neural network (CNN) for multi‐organ segmentation in abdomen CT images. The proposed model has a similar structure to V‐net, while a proposed MLP‐Convolutional block replaces each convolutional block. The MLP‐Convolutional block consists of three components: an early convolutional block for local features extraction and feature resampling, a token‐based MLP‐Mixer layer for capturing global features with high efficiency, and a token projector for pixel‐level detail recovery. We evaluate our proposed network using: (1) an institutional dataset with 60 patient cases and (2) a public dataset (BCTV) with 30 patient cases. The network performance was quantitatively evaluated in three domains: (1) volume similarity between the ground truth contours and the network predictions using the Dice score coefficient (DSC), sensitivity, and precision; (2) surface similarity using Hausdorff distance (HD), mean surface distance (MSD) and residual mean square distance (RMS); and (3) the computational complexity reported by the number of network parameters, training time, and inference time. The performance of the proposed network is compared with other state‐of‐the‐art networks.

Results

In the institutional dataset, the proposed network achieved the following volume similarity measures when averaged over all organs: DSC = 0.912, sensitivity = 0.917, precision = 0.917, average surface similarities were HD = 11.95 mm, MSD = 1.90 mm, RMS = 3.86 mm. The proposed network achieved DSC = 0.786 and HD = 9.04 mm on the public dataset. The network also shows statistically significant improvement, which is evaluated by a two‐tailed Wilcoxon Mann–Whitney U test, on right lung (MSD where the maximum p‐value is 0.001), spinal cord (sensitivity, precision, HD, RMSD where p‐value ranges from 0.001 to 0.039), and stomach (DSC where the maximum p‐value is 0.01) over all other competing networks. On the public dataset, the network report statistically significant improvement, which is shown by the Wilcoxon Mann–Whitney test, on pancreas (HD where the maximum p‐value is 0.006), left (HD where the maximum p‐value is 0.022) and right adrenal glands (DSC where the maximum p‐value is 0.026). In both datasets, the proposed method can generate contours in less than 5 s. Overall, the proposed MLP‐Vnet demonstrates comparable or better performance than competing methods with much lower memory complexity and higher speed.

Conclusions

The proposed MLP‐Vnet demonstrates superior segmentation performance, in terms of accuracy and efficiency, relative to state‐of‐the‐art methods. This reliable and efficient method demonstrates potential to streamline clinical workflows in abdominal radiotherapy, which may be especially important for online adaptive treatments.