Graph neural networks for automatic extraction and labeling of the coronary artery tree in CT angiography.

Purpose: Automatic comprehensive reporting of coronary artery disease (CAD) requires anatomical localization of the coronary artery pathologies. To address this, we propose a fully automatic method for extraction and anatomical labeling of the coronary artery tree using deep learning. Approach: We include coronary CT angiography (CCTA) scans of 104 patients from two hospitals. Reference annotations of coronary artery tree centerlines and labels of coronary artery segments were assigned to 10 segment classes following the American Heart Association guidelines. Our automatic method first extracts the coronary artery tree from CCTA, automatically placing a large number of seed points and simultaneous tracking of vessel-like structures from these points. Thereafter, the extracted tree is refined to retain coronary arteries only, which are subsequently labeled with a multi-resolution ensemble of graph convolutional neural networks that combine geometrical and image intensity information from adjacent segments. Results: The method is evaluated on its ability to extract the coronary tree and to label its segments, by comparing the automatically derived and the reference labels. A separate assessment of tree extraction yielded an F1 score of 0.85. Evaluation of our combined method leads to an average F1 score of 0.74. Conclusions: The results demonstrate that our method enables fully automatic extraction and anatomical labeling of coronary artery trees from CCTA scans. Therefore, it has the potential to facilitate detailed automatic reporting of CAD.

Automatic Coronary Artery Plaque Quantification and CAD-RADS Prediction Using Mesh Priors.

Coronary artery disease (CAD) remains the leading cause of death worldwide. Patients with suspected CAD undergo coronary CT angiography (CCTA) to evaluate the risk of cardiovascular events and determine the treatment. Clinical analysis of coronary arteries in CCTA comprises the identification of atherosclerotic plaque, as well as the grading of any coronary artery stenosis typically obtained through the CAD-Reporting and Data System (CAD-RADS). This requires analysis of the coronary lumen and plaque. While voxel-wise segmentation is a commonly used approach in various segmentation tasks, it does not guarantee topologically plausible shapes. To address this, in this work, we propose to directly infer surface meshes for coronary artery lumen and plaque based on a centerline prior and use it in the downstream task of CAD-RADS scoring. The method is developed and evaluated using a total of 2407 CCTA scans. Our method achieved lesion-wise volume intraclass correlation coefficients of 0.98, 0.79, and 0.85 for calcified, non-calcified, and total plaque volume respectively. Patient-level CAD-RADS categorization was evaluated on a representative hold-out test set of 300 scans, for which the achieved linearly weighted kappa ( κ ) was 0.75. CAD-RADS categorization on the set of 658 scans from another hospital and scanner led to a κ of 0.71. The results demonstrate that direct inference of coronary artery meshes for lumen and plaque is feasible, and allows for the automated prediction of routinely performed CAD-RADS categorization.

Deep learning-based detection of functionally significant stenosis in coronary CT angiography.

Patients with intermediate anatomical degree of coronary artery stenosis require determination of its functional significance. Currently, the reference standard for determining the functional significance of a stenosis is invasive measurement of the fractional flow reserve (FFR), which is associated with high cost and patient burden. To address these drawbacks, FFR can be predicted non-invasively from a coronary CT angiography (CCTA) scan. Hence, we propose a deep learning method for predicting the invasively measured FFR of an artery using a CCTA scan. The study includes CCTA scans of 569 patients from three hospitals. As reference for the functional significance of stenosis, FFR was measured in 514 arteries in 369 patients, and in the remaining 200 patients, obstructive coronary artery disease was ruled out by Coronary Artery Disease-Reporting and Data System (CAD-RADS) category 0 or 1. For prediction, the coronary tree is first extracted and used to reconstruct an MPR for the artery at hand. Thereafter, the coronary artery is characterized by its lumen, its attenuation and the area of the coronary artery calcium in each artery cross-section extracted from the MPR using a CNN. Additionally, characteristics indicating the presence of bifurcations and information indicating whether the artery is a main branch or a side-branch of a main artery are derived from the coronary artery tree. All characteristics are fed to a second network that predicts the FFR value and classifies the presence of functionally significant stenosis. The final result is obtained by merging the two predictions. Performance of our method is evaluated on held out test sets from multiple centers and vendors. The method achieves an area under the receiver operating characteristics curve (AUC) of 0.78, outperforming other works that do not require manual correction of the segmentation of the artery. This demonstrates that our method may reduce the number of patients that unnecessarily undergo invasive measurements.

Investigating the challenges and generalizability of deep learning brain conductivity mapping.

To investigate deep learning electrical properties tomography (EPT) for application on different simulated and in-vivo datasets, including pathologies for brain conductivity reconstructions, 3D patch-based convolutional neural networks were trained to predict conductivity maps from B 1 transceive phase data. To compare the performance of DL-EPT networks on different datasets, three datasets were used throughout this work, one from simulations and two from in-vivo measurements from healthy volunteers and patients with brain lesions, respectively. At first, networks trained on simulations were tested on all datasets with different levels of homogeneous Gaussian noise introduced in training and testing. Secondly, to investigate potential robustness towards systematical differences between simulated and measured phase maps, in-vivo data with conductivity labels from conventional EPT were used for training. High quality conductivity reconstructions from networks trained on simulations with and without noise confirm the potential of deep learning for EPT. However, when this network is used for in-vivo reconstructions, measurement related artifacts affect the quality of conductivity maps. Training DL-EPT networks using conductivity labels from conventional EPT improves the quality of the results. Networks trained on realistic simulations yield reconstruction artifacts when applied to in-vivo data. Training with realistic phase data and conductivity labels from conventional EPT allows for reducing these artifacts.

Machine Learning for Assessment of Coronary Artery Disease in Cardiac CT: A Survey.

Cardiac computed tomography (CT) allows rapid visualization of the heart and coronary arteries with high spatial resolution. However, analysis of cardiac CT scans for manifestation of coronary artery disease is time-consuming and challenging. Machine learning (ML) approaches have the potential to address these challenges with high accuracy and consistent performance. In this mini review, we present a survey of the literature on ML-based analysis of coronary artery disease in cardiac CT. We summarize ML methods for detection and characterization of atherosclerotic plaque as well as anatomically and functionally significant coronary artery stenosis.

Dictionary-based electric properties tomography.

PURPOSE: To develop and validate a new algorithm called "dictionary-based electric properties tomography" (dbEPT) for deriving tissue electric properties from measured B1 maps. METHODS: Inspired by Magnetic Resonance fingerprinting, dbEPT uses a dictionary of local patterns ("atoms") of B1 maps and corresponding electric properties distributions, derived from electromagnetic field simulations. For reconstruction, a pattern from a measured B1 map is compared with the B1 atoms of the dictionary. The B1 atom showing the best match with the measured B1 pattern yields the optimum electric properties pattern that is chosen for reconstruction. Matching was performed through machine learning algorithms. Two dictionaries, using transmit and transceive phases, were evaluated. The spatial distribution of local matching distance between optimal atom and measured pattern yielded a reconstruction reliability map. The method was applied to reconstruct conductivity of 4 volunteers' brains. A conventional, Helmholtz-based Electric properties tomography (EPT) reconstruction was performed for reference. Noise performance was studied through phantom simulations. RESULTS: Quantitative values of conductivity agree with literature values. Results of the 2 dictionaries exhibit only minor differences. Somewhat larger differences are visible between dbEPT and Helmholtz-based EPT. Quantified by the correlation between conductivity and anatomic images, dbEPT depicts brain details more clearly than Helmholtz-based EPT. Matching distance is minimal in homogeneous brain ventricles and increases with tissue heterogeneity. Central processing unit time was approximately 2 minutes per dictionary training and 3 minutes per brain conductivity reconstruction using standard hardware equipment. CONCLUSION: A new, dictionary-based approach for reconstructing electric properties is presented. Its conductivity reconstruction is able to overcome the EPT transceive-phase problem.