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Register a new userDetecting intracranial aneurysm rupture from 3D surfaces using a novel GraphNet approach
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Intracranial aneurysm (IA) is a life-threatening blood spot in humans brain if it ruptures and causes cerebral hemorrhage. It is challenging to detect whether an IA has ruptured from medical images. In this paper, we propose a novel graph based neural network named GraphNet to detect IA rupture from 3D surface data. GraphNet is based on graph convolution network (GCN) and is designed for graph-level classification and node-level segmentation. The network uses GCN blocks to extract surface local features and pools to global features. 1250 patient data including 385 ruptured and 865 unruptured IAs were collected from clinic for experiments. The performance on randomly selected 234 test patient data was reported. The experiment with the proposed GraphNet achieved accuracy of 0.82, area-under-curve (AUC) of receiver operating characteristic (ROC) curve 0.82 in the classification task, significantly outperforming the baseline approach without using graph based networks. The segmentation output of the model achieved mean graph-node-based dice coefficient (DSC) score 0.88.
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Automated segmentation of intracranial arteries on magnetic resonance angiography (MRA) allows for quantification of cerebrovascular features, which provides tools for understanding aging and pathophysiological adaptations of the cerebrovascular system. Using a convolutional autoencoder (CAE) for segmentation is promising as it takes advantage of the autoencoder structure in effective noise reduction and feature extraction by representing high dimensional information with low dimensional latent variables. In this report, an optimized CAE model (Y-net) was trained to learn a 3D segmentation model of intracranial arteries from 49 cases of MRA data. The trained model was shown to perform better than the three traditional segmentation methods in both binary classification and visual evaluation.
Enodvascular coils treat intracranial aneurysms (IAs) by causing them to occlude by thrombosis. Ideally, coiled IAs eventually occlude in the long-term. However, 20.8% are found incompletely occluded at treatment follow-up. Computer simulations of coiling and its effect on aneurysmal flow could help clinicians predict treatment outcomes a priori, but it requires accurate modeling of coils and their deployment procedure. In addition to being accurate, coiling simulations must be efficient to be used as a bedside tool. To date, several virtual coiling techniques have been developed, but they lack either accuracy or efficiency. For example, finite-element-based virtual coiling methods model the mechanics of coiling and are highly accurate, at the expense of high computational cost (and thus low efficiency). Geometric-rule-based coiling techniques ignore the mechanics and therefore are computationally efficient, but may produce unrealistic coil deployments. In order to develop a virtual coiling method that combines accuracy and efficiency, we propose a novel virtual coiling algorithm that models coil deployment with nonlinear mechanics and nonlinear contact. Our approach is potentially more accurate than existing simple techniques because we model coil mechanics. It is also potentially faster than finite-element techniques because it models the most time-consuming part of these algorithms-namely contact resolution-with a novel formulation that resolves contact faster with exponential functions. Moreover, we model the coils pre-shape as well as coil packaging into the catheter, both of which are important to model but are lacking from most existing techniques.
In stable coronary artery disease (CAD), reduction in mortality and/or myocardial infarction with revascularization over medical therapy has not been reliably achieved. Coronary arteries are usually extracted to perform stenosis detection. We aim to develop an automatic algorithm by deep learning to extract coronary arteries from ICAs.In this study, a multi-input and multi-scale (MIMS) U-Net with a two-stage recurrent training strategy was proposed for the automatic vessel segmentation. Incorporating features such as the Inception residual module with depth-wise separable convolutional layers, the proposed model generated a refined prediction map with the following two training stages: (i) Stage I coarsely segmented the major coronary arteries from pre-processed single-channel ICAs and generated the probability map of vessels; (ii) during the Stage II, a three-channel image consisting of the original preprocessed image, a generated probability map, and an edge-enhanced image generated from the preprocessed image was fed to the proposed MIMS U-Net to produce the final segmentation probability map. During the training stage, the probability maps were iteratively and recurrently updated by feeding into the neural network. After segmentation, an arterial stenosis detection algorithm was developed to extract vascular centerlines and calculate arterial diameters to evaluate stenotic level. Experimental results demonstrated that the proposed method achieved an average Dice score of 0.8329, an average sensitivity of 0.8281, and an average specificity of 0.9979 in our dataset with 294 ICAs obtained from 73 patient. Moreover, our stenosis detection algorithm achieved a true positive rate of 0.6668 and a positive predictive value of 0.7043.
Purpose: To leverage volumetric quantification of airspace disease (AD) derived from a superior modality (CT) serving as ground truth, projected onto digitally reconstructed radiographs (DRRs) to: 1) train a convolutional neural network to quantify airspace disease on paired CXRs; and 2) compare the DRR-trained CNN to expert human readers in the CXR evaluation of patients with confirmed COVID-19. Materials and Methods: We retrospectively selected a cohort of 86 COVID-19 patients (with positive RT-PCR), from March-May 2020 at a tertiary hospital in the northeastern USA, who underwent chest CT and CXR within 48 hrs. The ground truth volumetric percentage of COVID-19 related AD (POv) was established by manual AD segmentation on CT. The resulting 3D masks were projected into 2D anterior-posterior digitally reconstructed radiographs (DRR) to compute area-based AD percentage (POa). A convolutional neural network (CNN) was trained with DRR images generated from a larger-scale CT dataset of COVID-19 and non-COVID-19 patients, automatically segmenting lungs, AD and quantifying POa on CXR. CNN POa results were compared to POa quantified on CXR by two expert readers and to the POv ground-truth, by computing correlations and mean absolute errors. Results: Bootstrap mean absolute error (MAE) and correlations between POa and POv were 11.98% [11.05%-12.47%] and 0.77 [0.70-0.82] for average of expert readers, and 9.56%-9.78% [8.83%-10.22%] and 0.78-0.81 [0.73-0.85] for the CNN, respectively. Conclusion: Our CNN trained with DRR using CT-derived airspace quantification achieved expert radiologist level of accuracy in the quantification of airspace disease on CXR, in patients with positive RT-PCR for COVID-19.
To improve the performance of most neuroimiage analysis pipelines, brain extraction is used as a fundamental first step in the image processing. But in the case of fetal brain development, there is a need for a reliable US-specific tool. In this work we propose a fully automated 3D CNN approach to fetal brain extraction from 3D US clinical volumes with minimal preprocessing. Our method accurately and reliably extracts the brain regardless of the large data variation inherent in this imaging modality. It also performs consistently throughout a gestational age range between 14 and 31 weeks, regardless of the pose variation of the subject, the scale, and even partial feature-obstruction in the image, outperforming all current alternatives.
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