Three-dimensional multipath DenseNet for improving automatic segmentation of glioblastoma on pre-operative multimodal MR images

Abstract

Purpose: Convolutional neural networks have achieved excellent results in automatic medical image segmentation. In this study, we proposed a novel three-dimensional (3D) multipath DenseNet for generating the accurate glioblastoma (GBM) tumor contour from four multimodal pre-operative MR images. We hypothesized that the multipath architecture could achieve more accurate segmentation than a singlepath architecture.

Methods: Two hundred and fifty-eight GBM patients were included in this study. Each patient had four MR images (T1-weighted, contrast-enhanced T1-weighted, T2-weighted, and FLAIR) and the manually segmented tumor contour. We built a 3D multipath DenseNet that could be trained to achieve an end-to-end mapping from four MR images to the corresponding GBM tumor contour. A 3D singlepath DenseNet was also built for comparison. Both DenseNets were based on the encoder-decoder architecture. All four images were concatenated and fed into a single encoder path in the singlepath DenseNet, while each input image had its own encoder path in the multipath DenseNet. The patient cohort was randomly split into a training set of 180 patients, a validation set of 39 patients, and a testing set of 39 patients. Model performance was evaluated using the Dice similarity coefficient (DSC), average surface distance (ASD), and 95% Hausdorff distance (HD_95% ). Wilcoxon signed-rank tests were conducted to assess statistical significances.

Results: The singlepath DenseNet achieved the DSC of 0.911 ± 0.060, ASD of 1.3 ± 0.7 mm, and HD_95% of 5.2 ± 7.1 mm, while the multipath DenseNet achieved the DSC of 0.922 ± 0.041, ASD of 1.1 ± 0.5 mm, and HD_95% of 3.9 ± 3.3 mm. The P-values of all Wilcoxon signed-rank tests were less than 0.05.

Conclusions: Both DenseNets generated GBM tumor contours in good agreement with the manually segmented contours from multimodal MR images. The multipath DenseNet achieved more accurate tumor segmentation than the singlepath DenseNet. Here presented the 3D multipath DenseNet that demonstrated an improved accuracy over comparable algorithms in the clinical task of GBM tumor segmentation.

Keywords: 3D CNN; GBM tumor segmentation; multipath architecture.