To achieve better segmentation of MR images, image restoration is typically used as a preprocessing step, especially for low-quality MR images. Recent studies have demonstrated that dictionary learning methods could achieve promising performance for both image restoration and image segmentation. These methods typically learn paired dictionaries of image patches from different sources and use a common sparse representation to characterize paired image patches, such as low-quality image patches and their corresponding high quality counterparts for the image restoration, and image patches and their corresponding segmentation labels for the image segmentation. Since learning these dictionaries jointly in a unified framework may improve the image restoration and segmentation simultaneously, we propose a coupled dictionary learning method to concurrently learn dictionaries for joint image restoration and image segmentation based on sparse representations in a multi-atlas image segmentation framework. Particularly, three dictionaries, including a dictionary of low quality image patches, a dictionary of high quality image patches, and a dictionary of segmentation label patches, are learned in a unified framework so that the learned dictionaries of image restoration and segmentation can benefit each other. Our method has been evaluated for segmenting the hippocampus in MR T1 images collected with scanners of different magnetic field strengths. The experimental results have demonstrated that our method achieved better image restoration and segmentation performance than state of the art dictionary learning and sparse representation based image restoration and image segmentation methods.
Multi-atlas based image segmentation in conjunction with pattern recognition based label fusion strategies has achieved promising performance in a variety of image segmentation problems, including hippocampus segmentation from MR images. The pattern recognition based label fusion consists of image feature extraction and pattern recognition components. Since the feature extraction component plays an important role in the pattern recognition based label fusion, a variety of feature extraction methods have been proposed to extract image features, including texture features and random projection features. However, these feature extraction methods are not adaptive to different segmentation problems. Following the success of convolutional neural networks in image feature extraction, we propose a feature extraction method based on convolutional neural networks for multi-atlas based image segmentation. The proposed method has been validated based on 135 T1 magnetic resonance imaging (MRI) scans and their hippocampus labels provided by the EADC-ADNI harmonized segmentation protocol. We also compared our method with state-of-the-art pattern recognition based MAIS methods, including Local Label Learning and Random Local Binary Patterns. The experimental results have demonstrated that our method could achieve competitive hippocampus segmentation performance over the alternative methods under comparison.