This study investigates a 3D and fully convolutional neural network (CNN) for subcortical brain structure segmentation in MRI. 3D CNN architectures have been generally avoided due to their computational and memory requirements during inference. We address the problem via small kernels, allowing deeper architectures. We further model 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. Our model is efficiently trained end-to-end on a graphics processing unit (GPU), in a single stage, exploiting the dense inference capabilities of fully CNNs. We performed comprehensive experiments over two publicly available data sets. First, we demonstrate a state-of-the-art performance on the ISBR dataset. Then, we report a {\em large-scale} multi-site evaluation over 1112 unregistered subject data sets acquired from 17 different sites (ABIDE data set), with ages ranging from 7 to 64 years, showing that our method is robust to various acquisition protocols, demographics and clinical factors. Our method yielded segmentations that are highly consistent with a standard atlas-based approach, while running in a fraction of the time needed by atlas-based methods and avoiding registration/normalization steps. This makes it convenient for massive multi-site neuroanatomical imaging studies. To the best of our knowledge, our work is the first to study subcortical structure segmentation on such large-scale and heterogeneous data.

本研究针对MRI中的次皮质脑结构分割，提出了一种3D全卷积神经网络。通过采用小核允许更深层次的架构，将中间层输出嵌入到最终预测中，提高了特征提取的一致性和细粒度信息的准确性。在两个公开数据集上的实验表明，该方法在大规模神经解剖学成像研究中具有很强的鲁棒性和高效性。

MRI中基底核分割的3D卷积神经网络：一项大规模研究