Abstract Recent advances in deep learning methods have redefined the state-of-the-art for many medical imaging applications, surpassing previous approaches and sometimes even competing with human judgment in several tasks. Those models, however, when trained to reduce the empirical risk on a single domain, fail to generalize when applied to other domains, a very common scenario in medical imaging due to the variability of images and anatomical structures, even across the same imaging modality. In this work, we extend the method of unsupervised domain adaptation using self-ensembling for the semantic segmentation task and explore multiple facets of the method on a small and realistic publicly-available magnetic resonance (MRI) dataset. Through an extensive evaluation, we show that self-ensembling can indeed improve the generalization of the models even when using a small amount of unlabeled data.
Deep learning based methods for segmentation in medical imaging are being vastly explored in recent years @cite_40 and may vary in the specifics on how they handle the task. Most of the initial work was focused on patch-based segmentation @cite_50 , preceding the pioneering deep learning models. With the growing interest on deep learning for several computer vision tasks, the first attempts on using Convolutional Neural Networks (CNNs) for image segmentation were based on processing image patches through a sliding window, which yielded segmented patches. Those independent segmented patches were then concatenated for the creation of the final segmented image @cite_23 . The main drawbacks of this approach are regarding computational cost -- several forward passes for generating the final result -- as well as regarding inconsistency in predictions -- which can be fixed by overlapping sliding windows.
@cite_40 @cite_23 @cite_50
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Abstract Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks. Concise overviews are provided of studies per application area: neuro, retinal, pulmonary, digital pathology, breast, cardiac, abdominal, musculoskelet al. We end with a summary of the current state-of-the-art, a critical discussion of open challenges and directions for future research. This report provides an overview of the current state of the art deep learning architectures and optimisation techniques, and uses the ADNI hippocampus MRI dataset as an example to compare the effectiveness and efficiency of different convolutional architectures on the task of patch-based 3-dimensional hippocampal segmentation, which is important in the diagnosis of Alzheimer's Disease. We found that a slightly unconventional "stacked 2D" approach provides much better classification performance than simple 2D patches without requiring significantly more computational power. We also examined the popular "tri-planar" approach used in some recently published studies, and found that it provides much better results than the 2D approaches, but also with a moderate increase in computational power requirement. Finally, we evaluated a full 3D convolutional architecture, and found that it provides marginally better results than the tri-planar approach, but at the cost of a very significant increase in computational power requirement. Quantitative magnetic resonance analysis often requires accurate, robust, and reliable automatic extraction of anatomical structures. Recently, template-warping methods incorporating a label fusion strategy have demonstrated high accuracy in segmenting cerebral structures. In this study, we propose a novel patch-based method using expert manual segmentations as priors to achieve this task. Inspired by recent work in image denoising, the proposed nonlocal patch-based label fusion produces accurate and robust segmentation. Validation with two different datasets is presented. In our experiments, the hippocampi of 80 healthy subjects and the lateral ventricles of 80 patients with Alzheimer's disease were segmented. The influence on segmentation accuracy of different parameters such as patch size and number of training subjects was also studied. A comparison with an appearance-based method and a template-based method was also carried out. The highest median kappa index values obtained with the proposed method were 0.884 for hippocampus segmentation and 0.959 for lateral ventricle segmentation.