FD-FCN: 3D Fully Dense and Fully Convolutional Network for Semantic Segmentation of Brain Anatomy

In this paper, a 3D patch-based fully dense and fully convolutional network (FD-FCN) is proposed for fast and accurate segmentation of subcortical structures in T1-weighted magnetic resonance images. Developed from the seminal FCN with an end-to-end learning-based approach and constructed by newly designed dense blocks including a dense fully-connected layer, the proposed FD-FCN is different from other FCN-based methods and leads to an outperformance in the perspective of both efficiency and accuracy. Compared with the U-shaped architecture, FD-FCN discards the upsampling path for model fitness. To alleviate the problem of parameter explosion, the inputs of dense blocks are no longer directly passed to subsequent layers. This architecture of FD-FCN brings a great reduction on both memory and time consumption in training process. Although FD-FCN is slimmed down, in model competence it gains better capability of dense inference than other conventional networks. This benefits from the construction of network architecture and the incorporation of redesigned dense blocks. The multi-scale FD-FCN models both local and global context by embedding intermediate-layer outputs in the final prediction, which encourages consistency between features extracted at different scales and embeds fine-grained information directly in the segmentation process. In addition, dense blocks are rebuilt to enlarge the receptive fields without significantly increasing parameters, and spectral coordinates are exploited for spatial context of the original input patch. The experiments were performed over the IBSR dataset, and FD-FCN produced an accurate segmentation result of overall Dice overlap value of 89.81% for 11 brain structures in 53 seconds, with at least 3.66% absolute improvement of dice accuracy than state-of-the-art 3D FCN-based methods.