Fully automated prostate whole gland and central gland segmentation on MRI using holistically nested networks with short connections

J Med Imaging (Bellingham). 2019 Apr;6(2):024007. doi: 10.1117/1.JMI.6.2.024007. Epub 2019 Jun 5.


Accurate and automated prostate whole gland and central gland segmentations on MR images are essential for aiding any prostate cancer diagnosis system. Our work presents a 2-D orthogonal deep learning method to automatically segment the whole prostate and central gland from T2-weighted axial-only MR images. The proposed method can generate high-density 3-D surfaces from low-resolution ( z axis) MR images. In the past, most methods have focused on axial images alone, e.g., 2-D based segmentation of the prostate from each 2-D slice. Those methods suffer the problems of over-segmenting or under-segmenting the prostate at apex and base, which adds a major contribution for errors. The proposed method leverages the orthogonal context to effectively reduce the apex and base segmentation ambiguities. It also overcomes jittering or stair-step surface artifacts when constructing a 3-D surface from 2-D segmentation or direct 3-D segmentation approaches, such as 3-D U-Net. The experimental results demonstrate that the proposed method achieves 92.4 % ± 3 % Dice similarity coefficient (DSC) for prostate and DSC of 90.1 % ± 4.6 % for central gland without trimming any ending contours at apex and base. The experiments illustrate the feasibility and robustness of the 2-D-based holistically nested networks with short connections method for MR prostate and central gland segmentation. The proposed method achieves segmentation results on par with the current literature.

Keywords: MRI; deep learning; holistically nested networks; prostate; segmentation.