In this paper we present a method for simultaneously segmenting brain tumors and an extensive set of organs-at-risk for radiation therapy planning of glioblastomas. The method combines a contrast-adaptive generative model for whole-brain segmentation with a new spatial regularization model of tumor shape using convolutional restricted Boltzmann machines. We demonstrate experimentally that the method is able to adapt to image acquisitions that differ substantially from any available training data, ensuring its applicability across treatment sites; that its tumor segmentation accuracy is comparable to that of the current state of the art; and that it captures most organs-at-risk sufficiently well for radiation therapy planning purposes. The proposed method may be a valuable step towards automating the delineation of brain tumors and organs-at-risk in glioblastoma patients undergoing radiation therapy.
We propose a segmentation framework that uses deep neural networks and introduce two innovations. First, we describe a biophysics-based domain adaptation method. Second, we propose an automatic method to segment white and gray matter, and cerebrospinal fluid, in addition to tumorous tissue. Regarding our first innovation, we use a domain adaptation framework that combines a novel multispecies biophysical tumor growth model with a generative adversarial model to create realistic looking synthetic multimodal MR images with known segmentation. Regarding our second innovation, we propose an automatic approach to enrich available segmentation data by computing the segmentation for healthy tissues. This segmentation, which is done using diffeomorphic image registration between the BraTS training data and a set of prelabeled atlases, provides more information for training and reduces the class imbalance problem. Our overall approach is not specific to any particular neural network and can be used in conjunction with existing solutions. We demonstrate the performance improvement using a 2D U-Net for the BraTS'18 segmentation challenge. Our biophysics based domain adaptation achieves better results, as compared to the existing state-of-the-art GAN model used to create synthetic data for training.
In this paper, we present a fully automatic brain tumor segmentation method based on Deep Neural Networks (DNNs). The proposed networks are tailored to glioblastomas (both low and high grade) pictured in MR images. By their very nature, these tumors can appear anywhere in the brain and have almost any kind of shape, size, and contrast. These reasons motivate our exploration of a machine learning solution that exploits a flexible, high capacity DNN while being extremely efficient. Here, we give a description of different model choices that we've found to be necessary for obtaining competitive performance. We explore in particular different architectures based on Convolutional Neural Networks (CNN), i.e. DNNs specifically adapted to image data. We present a novel CNN architecture which differs from those traditionally used in computer vision. Our CNN exploits both local features as well as more global contextual features simultaneously. Also, different from most traditional uses of CNNs, our networks use a final layer that is a convolutional implementation of a fully connected layer which allows a 40 fold speed up. We also describe a 2-phase training procedure that allows us to tackle difficulties related to the imbalance of tumor labels. Finally, we explore a cascade architecture in which the output of a basic CNN is treated as an additional source of information for a subsequent CNN. Results reported on the 2013 BRATS test dataset reveal that our architecture improves over the currently published state-of-the-art while being over 30 times faster.
Black, M.D., Ph.D., E. Alexander, III, M.D., F. Jolesz, M.D. Localization of tumors in brain surgery is one of the most challenging aspects of the field. In difficult cases involving small or deep tumors localization has traditionally been achieved using a stereolactic frame rigidly fixed to the patient's skull. We have developed an enhanced reality technique that simplifies tumor localization in brain surgery s. The technique involves merging three dimensional (3D) computereconstructed preoperative medical scans with live peri-operative video images of patients. This image fusion combines the information from the preoperative study with the operative field in a medium readily accessible to surgeons.
Class imbalance has been one of the major challenges for medical image segmentation. The model cascade (MC) strategy significantly alleviates class imbalance issue. In spite of its outstanding performance, this method leads to an undesired system complexity and meanwhile ignores the relevance among the models. To handle these flaws of MC, we propose in this paper a light-weight deep model, i.e., the One-pass Multi-task Network (OM-Net) to solve class imbalance better than MC and require only one-pass computation for brain tumor segmentation. First, OM-Net integrates the separate segmentation tasks into one deep model. Second, to optimize OM-Net more effectively, we take advantage of the correlation among tasks to design an online training data transfer strategy and a curriculum learning-based training strategy. Third, we further propose to share prediction results between tasks, which enables us to design a cross-task guided attention (CGA) module. With the guidance of prediction results provided by the previous task, CGA can adaptively recalibrate channel-wise feature responses based on the category-specific statistics. Finally, a simple yet effective post-processing method is introduced to refine the segmentation results of the proposed attention network. Extensive experiments are performed to justify the effectiveness of the proposed techniques. Most impressively, we achieve state-of-the-art performance on the BraTS 2015 and BraTS 2017 datasets. With the proposed approaches, we also won the joint third place in the BraTS 2018 challenge among 64 participating teams. We will make the code publicly available at https://github.com/chenhong-zhou/OM-Net.