In the isointense stage, the accurate volumetric image segmentation is a challenging task due to the low contrast between tissues. In this paper, we propose a novel very deep network architecture based on a densely convolutional network for volumetric brain segmentation. The proposed network architecture provides a dense connection between layers that aims to improve the information flow in the network. By concatenating features map of fine and coarse dense blocks, it allows capturing multi-scale contextual information. Experimental results demonstrate significant advantages of the proposed method over existing methods, in terms of both segmentation accuracy and parameter efficiency in MICCAI grand challenge on 6-month infant brain MRI segmentation.
Precise 3D segmentation of infant brain tissues is an essential step towards comprehensive volumetric studies and quantitative analysis of early brain developement. However, computing such segmentations is very challenging, especially for 6-month infant brain, due to the poor image quality, among other difficulties inherent to infant brain MRI, e.g., the isointense contrast between white and gray matter and the severe partial volume effect due to small brain sizes. This study investigates the problem with an ensemble of semi-dense fully convolutional neural networks (CNNs), which employs T1-weighted and T2-weighted MR images as input. We demonstrate that the ensemble agreement is highly correlated with the segmentation errors. Therefore, our method provides measures that can guide local user corrections. To the best of our knowledge, this work is the first ensemble of 3D CNNs for suggesting annotations within images. Furthermore, inspired by the very recent success of dense networks, we propose a novel architecture, SemiDenseNet, which connects all convolutional layers directly to the end of the network. Our architecture allows the efficient propagation of gradients during training, while limiting the number of parameters, requiring one order of magnitude less parameters than popular medical image segmentation networks such as 3D U-Net. Another contribution of our work is the study of the impact that early or late fusions of multiple image modalities might have on the performances of deep architectures. We report evaluations of our method on the public data of the MICCAI iSEG-2017 Challenge on 6-month infant brain MRI segmentation, and show very competitive results among 21 teams, ranking first or second in most metrics.
Neonatal brain segmentation in magnetic resonance (MR) is a challenging problem due to poor image quality and low contrast between white and gray matter regions. Most existing approaches for this problem are based on multi-atlas label fusion strategies, which are time-consuming and sensitive to registration errors. As alternative to these methods, we propose a hyper-densely connected 3D convolutional neural network that employs MR-T1 and T2 images as input, which are processed independently in two separated paths. An important difference with previous densely connected networks is the use of direct connections between layers from the same and different paths. Adopting such dense connectivity helps the learning process by including deep supervision and improving gradient flow. We evaluated our approach on data from the MICCAI Grand Challenge on 6-month infant Brain MRI Segmentation (iSEG), obtaining very competitive results. Among 21 teams, our approach ranked first or second in most metrics, translating into a state-of-the-art performance.