Multi-stream 3D FCN with multi-scale deep supervision for multi-modality isointense infant brain MR image segmentation

We present a method to address the challenging problem of segmentation of multi-modality isointense infant brain MR images into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF). Our method is based on context-guided, multi-stream fully convolutional networks (FCN), which after training, can directly map a whole volumetric data to its volume-wise labels. In order to alleviate the potential gradient vanishing problem during training, we designed multi-scale deep supervision. Furthermore, context information was used to further improve the performance of our method. Validated on the test data of the MICCAI 2017 Grand Challenge on 6-month infant brain MRI segmentation (iSeg-2017), our method achieved an average Dice Overlap Coefficient of 95.4%, 91.6% and 89.6% for CSF, GM and WM, respectively.