A deep learning-based segmentation method for brain tumor in MR images

Accurate tumor segmentation is an essential and crucial step for computer-aided brain tumor diagnosis and surgical planning. Subjective segmentations are widely adopted in clinical diagnosis and treating, but they are neither accurate nor reliable. An automatical and objective system for brain tumor segmentation is strongly expected. But they are still facing some challenges such as lower segmentation accuracy, demanding a priori knowledge or requiring the human intervention. In this paper, a novel and new coarse-to-fine method is proposed to segment the brain tumor. This hierarchical framework consists of preprocessing, deep learning network based classification and post-processing. The preprocessing is used to extract image patches for each MR image and obtains the gray level sequences of image patches as the input of the deep learning network. The deep learning network based classification is implemented by a stacked auto-encoder network to extract the high level abstract feature from the input, and utilizes the extracted feature to classify image patches. After mapping the classification result to a binary image, the post-processing is implemented by a morphological filter to get the final segmentation result. In order to evaluate the proposed method, the experiment was applied to segment the brain tumor for the real patient dataset. The final performance shows that the proposed brain tumor segmentation method is more accurate and efficient.