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Register a new userAutomated quantification of myocardial tissue characteristics from native T1 mapping using neural networks with Bayesian inference for uncertainty-based quality-control
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Tissue characterisation with CMR parametric mapping has the potential to detect and quantify both focal and diffuse alterations in myocardial structure not assessable by late gadolinium enhancement. Native T1 mapping in particular has shown promise as a useful biomarker to support diagnostic, therapeutic and prognostic decision-making in ischaemic and non-ischaemic cardiomyopathies. Convolutional neural networks with Bayesian inference are a category of artificial neural networks which model the uncertainty of the network output. This study presents an automated framework for tissue characterisation from native ShMOLLI T1 mapping at 1.5T using a Probabilistic Hierarchical Segmentation (PHiSeg) network. In addition, we use the uncertainty information provided by the PHiSeg network in a novel automated quality control (QC) step to identify uncertain T1 values. The PHiSeg network and QC were validated against manual analysis on a cohort of the UK Biobank containing healthy subjects and chronic cardiomyopathy patients. We used the proposed method to obtain reference T1 ranges for the left ventricular myocardium in healthy subjects as well as common clinical cardiac conditions. T1 values computed from automatic and manual segmentations were highly correlated (r=0.97). Bland-Altman analysis showed good agreement between the automated and manual measurements. The average Dice metric was 0.84 for the left ventricular myocardium. The sensitivity of detection of erroneous outputs was 91%. Finally, T1 values were automatically derived from 14,683 CMR exams from the UK Biobank. The proposed pipeline allows for automatic analysis of myocardial native T1 mapping and includes a QC process to detect potentially erroneous results. T1 reference values were presented for healthy subjects and common clinical cardiac conditions from the largest cohort to date using T1-mapping images.
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Bayesian Neural Networks (BNNs) place priors over the parameters in a neural network. Inference in BNNs, however, is difficult; all inference methods for BNNs are approximate. In this work, we empirically compare the quality of predictive uncertainty estimates for 10 common inference methods on both regression and classification tasks. Our experiments demonstrate that commonly used metrics (e.g. test log-likelihood) can be misleading. Our experiments also indicate that inference innovations designed to capture structure in the posterior do not necessarily produce high quality posterior approximations.
Automatic myocardial segmentation of contrast echocardiography has shown great potential in the quantification of myocardial perfusion parameters. Segmentation quality control is an important step to ensure the accuracy of segmentation results for quality research as well as its clinical application. Usually, the segmentation quality control happens after the data acquisition. At the data acquisition time, the operator could not know the quality of the segmentation results. On-the-fly segmentation quality control could help the operator to adjust the ultrasound probe or retake data if the quality is unsatisfied, which can greatly reduce the effort of time-consuming manual correction. However, it is infeasible to deploy state-of-the-art DNN-based models because the segmentation module and quality control module must fit in the limited hardware resource on the ultrasound machine while satisfying strict latency constraints. In this paper, we propose a hardware-aware neural architecture search framework for automatic myocardial segmentation and quality control of contrast echocardiography. We explicitly incorporate the hardware latency as a regularization term into the loss function during training. The proposed method searches the best neural network architecture for the segmentation module and quality prediction module with strict latency.
Purpose: To demonstrate the feasibility and performance of a fully automated deep learning framework to estimate myocardial strain from short-axis cardiac magnetic resonance tagged images. Methods and Materials: In this retrospective cross-sectional study, 4508 cases from the UK Biobank were split randomly into 3244 training and 812 validation cases, and 452 test cases. Ground truth myocardial landmarks were defined and tracked by manual initialization and correction of deformable image registration using previously validated software with five readers. The fully automatic framework consisted of 1) a convolutional neural network (CNN) for localization, and 2) a combination of a recurrent neural network (RNN) and a CNN to detect and track the myocardial landmarks through the image sequence for each slice. Radial and circumferential strain were then calculated from the motion of the landmarks and averaged on a slice basis. Results: Within the test set, myocardial end-systolic circumferential Green strain errors were -0.001 +/- 0.025, -0.001 +/- 0.021, and 0.004 +/- 0.035 in basal, mid, and apical slices respectively (mean +/- std. dev. of differences between predicted and manual strain). The framework reproduced significant reductions in circumferential strain in diabetics, hypertensives, and participants with previous heart attack. Typical processing time was ~260 frames (~13 slices) per second on an NVIDIA Tesla K40 with 12GB RAM, compared with 6-8 minutes per slice for the manual analysis. Conclusions: The fully automated RNNCNN framework for analysis of myocardial strain enabled unbiased strain evaluation in a high-throughput workflow, with similar ability to distinguish impairment due to diabetes, hypertension, and previous heart attack.
Four-dimensional (4D) left ventricular myocardial velocity mapping (MVM) is a cardiac magnetic resonance (CMR) technique that allows assessment of cardiac motion in three orthogonal directions. Accurate and reproducible delineation of the myocardium is crucial for accurate analysis of peak systolic and diastolic myocardial velocities. In addition to the conventionally available magnitude CMR data, 4D MVM also acquires three velocity-encoded phase datasets which are used to generate velocity maps. These can be used to facilitate and improve myocardial delineation. Based on the success of deep learning in medical image processing, we propose a novel automated framework that improves the standard U-Net based methods on these CMR multi-channel data (magnitude and phase) by cross-channel fusion with attention module and shape information based post-processing to achieve accurate delineation of both epicardium and endocardium contours. To evaluate the results, we employ the widely used Dice scores and the quantification of myocardial longitudinal peak velocities. Our proposed network trained with multi-channel data shows enhanced performance compared to standard U-Net based networks trained with single-channel data. Based on the results, our method provides compelling evidence for the design and application for the multi-channel image analysis of the 4D MVM CMR data.
Solving partial differential equations (PDEs) is the canonical approach for understanding the behavior of physical systems. However, large scale solutions of PDEs using state of the art discretization techniques remains an expensive proposition. In this work, a new physics-constrained neural network (NN) approach is proposed to solve PDEs without labels, with a view to enabling high-throughput solutions in support of design and decision-making. Distinct from existing physics-informed NN approaches, where the strong form or weak form of PDEs are used to construct the loss function, we write the loss function of NNs based on the discretized residual of PDEs through an efficient, convolutional operator-based, and vectorized implementation. We explore an encoder-decoder NN structure for both deterministic and probabilistic models, with Bayesian NNs (BNNs) for the latter, which allow us to quantify both epistemic uncertainty from model parameters and aleatoric uncertainty from noise in the data. For BNNs, the discretized residual is used to construct the likelihood function. In our approach, both deterministic and probabilistic convolutional layers are used to learn the applied boundary conditions (BCs) and to detect the problem domain. As both Dirichlet and Neumann BCs are specified as inputs to NNs, a single NN can solve for similar physics, but with different BCs and on a number of problem domains. The trained surrogate PDE solvers can also make interpolating and extrapolating (to a certain extent) predictions for BCs that they were not exposed to during training. Such surrogate models are of particular importance for problems, where similar types of PDEs need to be repeatedly solved for many times with slight variations. We demonstrate the capability and performance of the proposed framework by applying it to steady-state diffusion, linear elasticity, and nonlinear elasticity.
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