M-net: A Convolutional Neural Network for deep brain structure segmentation

In this paper, we propose an end-to-end trainable Convolutional Neural Network (CNN) architecture called the M-net, for segmenting deep (human) brain structures from Magnetic Resonance Images (MRI). A novel scheme is used to learn to combine and represent 3D context information of a given slice in a 2D slice. Consequently, the M-net utilizes only 2D convolution though it operates on 3D data, which makes M-net memory efficient. The segmentation method is evaluated on two publicly available datasets and is compared against publicly available model based segmentation algorithms as well as other classification based algorithms such as Random Forrest and 2D CNN based approaches. Experiment results show that the M-net outperforms all these methods in terms of dice coefficient and is at least 3 times faster than other methods in segmenting a new volume which is attractive for clinical use.