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.
This paper analyzes the use of 3D Convolutional Neural Networks for brain tumor segmentation in MR images. We address the problem using three different architectures that combine fine and coarse features to obtain the final segmentation. We compare three different networks that use multi-resolution features in terms of both design and performance and we show that they improve their single-resolution counterparts.
Convolutional neural network (CNN) has been widely used for image processing tasks.In this paper we design a bottleneck supervised U-Net model and apply it to liver and tumor segmentation. Taking an image as input, the model outputs segmented images of the same size, each pixel of which takes value from 1 to K where K is the number of classes to be segmented. The innovations of this paper are two-fold: first we design a novel U-Net structure which include dense block and inception block as the base U-Net; second we design a double U-Net architecture based on the base U-Net and includes an encoding U-Net and a segmentation U-Net. The encoding U-Net is first trained to encode the labels, then the encodings are used to supervise the bottleneck of the segmentation U-Net. While training the segmentation U-Net, a weighted average of dice loss(for the final output) and MSE loss(for the bottleneck) is used as the overall loss function. This approach can help retain the hidden features of input images. The model is applied to a liver tumor 3D CT scan dataset to conduct liver and tumor segmentation sequentially. Experimental results indicate bottleneck supervised U-Net can accomplish segmentation tasks effectively with better performance in controlling shape distortion, reducing false positive and false negative, besides accelerating convergence. Besides, this model has good generalization for further improvement.
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.
Brain cancer can be very fatal, but chances of survival increase through early detection and treatment. Doctors use Magnetic Resonance Imaging (MRI) to detect and locate tumors in the brain, and very carefully analyze scans to segment brain tumors. Manual segmentation is time consuming and tiring for doctors, and it can be difficult for them to notice extremely small abnormalities. Automated segmentations performed by computers offer quicker diagnoses, the ability to notice small details, and more accurate segmentations. Advances in deep learning and computer hardware have allowed for high-performing automated segmentation approaches. However, several problems persist in practice: increased training time, class imbalance, and low performance. In this paper, I propose applying V-Net, a volumetric, fully convolutional neural network, to segment brain tumors in MRI scans from the BraTS Challenges. With this approach, I achieve a whole tumor dice score of 0.89 and train the network in a short time while addressing class imbalance with the use of a dice loss layer. Then, I propose applying an existing technique to improve automated segmentation performance in practice.