Automated CT and MRI Liver Segmentation and Biometry Using a Generalized Convolutional Neural Network.

PurposeTo assess feasibility of training a convolutional neural network (CNN) to automate liver segmentation across different imaging modalities and techniques used in clinical practice and apply this to enable automation of liver biometry.MethodsWe trained a 2D U-Net CNN for liver segmentation in two stages using 330 abdominal MRI and CT exams acquired at our institution. First, we trained the neural network with non-contrast multi-echo spoiled-gradient-echo (SGPR)images with 300 MRI exams to provide multiple signal-weightings. Then, we used transfer learning to generalize the CNN with additional images from 30 contrast-enhanced MRI and CT exams.We assessed the performance of the CNN using a distinct multi-institutional data set curated from multiple sources (n = 498 subjects). Segmentation accuracy was evaluated by computing Dice scores. Utilizing these segmentations, we computed liver volume from CT and T1-weighted (T1w) MRI exams, and estimated hepatic proton- density-fat-fraction (PDFF) from multi-echo T2*w MRI exams. We compared quantitative volumetry and PDFF estimates between automated and manual segmentation using Pearson correlation and Bland-Altman statistics.ResultsDice scores were 0.94 ± 0.06 for CT (n = 230), 0.95 ± 0.03 (n = 100) for T1w MR, and 0.92 ± 0.05 for T2*w MR (n = 169). Liver volume measured by manual and automated segmentation agreed closely for CT (95% limit-of-agreement (LoA) = [-298 mL, 180 mL]) and T1w MR (LoA = [-358 mL, 180 mL]). Hepatic PDFF measured by the two segmentations also agreed closely (LoA = [-0.62%, 0.80%]).ConclusionsUtilizing a transfer-learning strategy, we have demonstrated the feasibility of a CNN to be generalized to perform liver segmentations across different imaging techniques and modalities. With further refinement and validation, CNNs may have broad applicability for multimodal liver volumetry and hepatic tissue characterization

Brain Tumor Segmentation with Deep Neural Networks

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

DepthCut: Improved Depth Edge Estimation Using Multiple Unreliable Channels

In the context of scene understanding, a variety of methods exists to estimate different information channels from mono or stereo images, including disparity, depth, and normals. Although several advances have been reported in the recent years for these tasks, the estimated information is often imprecise particularly near depth discontinuities or creases. Studies have however shown that precisely such depth edges carry critical cues for the perception of shape, and play important roles in tasks like depth-based segmentation or foreground selection. Unfortunately, the currently extracted channels often carry conflicting signals, making it difficult for subsequent applications to effectively use them. In this paper, we focus on the problem of obtaining high-precision depth edges (i.e., depth contours and creases) by jointly analyzing such unreliable information channels. We propose DepthCut, a data-driven fusion of the channels using a convolutional neural network trained on a large dataset with known depth. The resulting depth edges can be used for segmentation, decomposing a scene into depth layers with relatively flat depth, or improving the accuracy of the depth estimate near depth edges by constraining its gradients to agree with these edges. Quantitatively, we compare against 15 variants of baselines and demonstrate that our depth edges result in an improved segmentation performance and an improved depth estimate near depth edges compared to data-agnostic channel fusion. Qualitatively, we demonstrate that the depth edges result in superior segmentation and depth orderings.Comment: 12 page

Deep Hierarchical Parsing for Semantic Segmentation

This paper proposes a learning-based approach to scene parsing inspired by the deep Recursive Context Propagation Network (RCPN). RCPN is a deep feed-forward neural network that utilizes the contextual information from the entire image, through bottom-up followed by top-down context propagation via random binary parse trees. This improves the feature representation of every super-pixel in the image for better classification into semantic categories. We analyze RCPN and propose two novel contributions to further improve the model. We first analyze the learning of RCPN parameters and discover the presence of bypass error paths in the computation graph of RCPN that can hinder contextual propagation. We propose to tackle this problem by including the classification loss of the internal nodes of the random parse trees in the original RCPN loss function. Secondly, we use an MRF on the parse tree nodes to model the hierarchical dependency present in the output. Both modifications provide performance boosts over the original RCPN and the new system achieves state-of-the-art performance on Stanford Background, SIFT-Flow and Daimler urban datasets.Comment: IEEE CVPR 201