Improved segmentation of basal ganglia from MR images using convolutional neural network with crossover-typed skip connection

Purpose Accurate and automatic segmentation of basal ganglia from magnetic resonance (MR) images is important for diagnosis and treatment of various brain disorders. However, the basal ganglia segmentation is a challenging task because of the class imbalance and the unclear boundaries among basal ganglia anatomical structures. Thus, we aim to present an encoder–decoder convolutional neural network (CNN)-based method for improved segmentation of basal ganglia by focusing on skip connections that determine the segmentation performance of encoder–decoder CNNs. We also aim to reveal the effect of skip connections on the segmentation of basal ganglia with unclear boundaries. Methods We used the encoder–decoder CNNs with the following five patterns of skip connections: without skip connection, with full-resolution horizontal skip connection, with horizontal skip connections, with vertical skip connections, and with crossover-typed skip connections (the proposed method). We compared and evaluated the performance of the CNNs in the experiment of basal ganglia segmentation using T1-weighted MR brain images of 79 patients. Results The experimental results showed that the skip connections at each scale level help CNNs to acquire multi-scale image features, the vertical skip connections contribute on acquiring finer image features for segmentation of smaller anatomical structures with more blurred boundaries, and the crossover-typed skip connections, a combination of horizontal and vertical skip connections, provided better segmentation accuracy. Conclusion This paper investigated the effect of skip connections on the basal ganglia segmentation and revealed the crossover-typed skip connections might be effective for improving the segmentation of basal ganglia with the class imbalance and the unclear boundaries.