End-to-end Segmentation with Recurrent Attention Neural Network.

Image segmentation quality depends heavily on the quality of the image. For many medical imaging modalities, image reconstruction is required to convert acquired raw data to images before any analysis. However, imperfect reconstruction with artifacts and loss of information is almost inevitable, which compromises the final performance of segmentation. In this study, we present a novel end-to-end deep learning framework that performs magnetic resonance brain image segmentation directly from the raw data. The end-to-end framework consists a unique task-driven attention module that recurrently utilizes intermediate segmentation result to facilitate image-domain feature extraction from the raw data for segmentation, thus closely bridging the reconstruction and the segmentation tasks. In addition, we introduce a novel workflow to generate labeled training data for segmentation by exploiting imaging modality simulators and digital phantoms. Extensive experiment results show that the proposed method outperforms the state-of-the-art methods.