Dominik Bernhardt

Detection, grading and classification of coronary stenoses in computed tomography angiography

Recently conducted clinical studies prove the utility of Coronary Computed Tomography Angiography (CCTA) as a viable alternative to invasive angiography for the detection of Coronary Artery Disease (CAD). This has lead to the development of several algorithms for automatic detection and grading of coronary stenoses. However, most of these methods focus on detecting calcified plaques only. A few methods that can also detect and grade non-calcified plaques require substantial user involvement. In this paper, we propose a fast and fully automatic system that is capable of detecting, grading and classifying coronary stenoses in CCTA caused by all types of plaques. We propose a four-step approach including a learning-based centerline verification step and a lumen cross-section estimation step using random regression forests. We show state-of-the-art performance of our method in experiments conducted on a set of 229 CCTA volumes. With an average processing time of 1.8 seconds per case after centerline extraction, our method is significantly faster than competing approaches.

Search strategies for multiple landmark detection by submodular maximization

A fundamental issue in multiple landmark detection is the reduction of computational cost. This problem has previously been addressed mainly by reducing the complexity of each individual landmark detector. We address the problem by optimizing the search strategy of multiple landmarks. When the relative positions of landmarks are constrained, the search space can be reduced, thereby reducing the computation. The proposed method leverages the theory of submodular functions to provide a constant factor approximation guarantee of the optimal speed. Although the theory of submodular functions is well known, to the best of our knowledge, this is the first time it is applied to the landmark detection problem. We demonstrate our method by fast and accurate detection of human body landmarks including bones, organs, and vessels in 3D CT images from a diverse dataset of around 2000 volumes with pathological patients. We further provide different search space criteria and variations.

A framework for personalization of coronary flow computations during rest and hyperemia

We introduce a Computational Fluid Dynamics (CFD) based method for performing patient-specific coronary hemodynamic computations under two conditions: at rest and during drug-induced hyperemia. The proposed method is based on a novel estimation procedure for determining the boundary conditions from non-invasively acquired patient data at rest. A multi-variable feedback control framework ensures that the computed mean arterial pressure and the flow distribution matches the estimated values for an individual patient during the rest state. The boundary conditions at hyperemia are derived from the respective rest-state values via a transfer function that models the vasodilation phenomenon. Simulations are performed on a coronary tree where a 65% diameter stenosis is introduced in the left anterior descending (LAD) artery, with the boundary conditions estimated using the proposed method. The results demonstrate that the estimation of the hyperemic resistances is crucial in order to obtain accurate values for pressure and flow rates. Results from an exhaustive sensitivity analysis have been presented for analyzing the variability of trans-stenotic pressure drop and Fractional Flow Reserve (FFR) values with respect to various measurements and assumptions.

Validation and detection of vessel landmarks by using anatomical knowledge

The detection of anatomical landmarks is an important prerequisite to analyze medical images fully automatically. Several machine learning approaches have been proposed to parse 3D CT datasets and to determine the location of landmarks with associated uncertainty. However, it is a challenging task to incorporate high-level anatomical knowledge to improve these classification results. We propose a new approach to validate candidates for vessel bifurcation landmarks which is also applied to systematically search missed and to validate ambiguous landmarks. A knowledge base is trained providing human-readable geometric information of the vascular system, mainly vessel lengths, radii and curvature information, for validation of landmarks and to guide the search process. To analyze the bifurcation area surrounding a vessel landmark of interest, a new approach is proposed which is based on Fast Marching and incorporates anatomical information from the knowledge base. Using the proposed algorithms, an anatomical knowledge base has been generated based on 90 manually annotated CT images containing different parts of the body. To evaluate the landmark validation a set of 50 carotid datasets has been tested in combination with a state of the art landmark detector with excellent results. Beside the carotid bifurcation the algorithm is designed to handle a wide range of vascular landmarks, e.g. celiac, superior mesenteric, renal, aortic, iliac and femoral bifurcation.

Fast automatic algorithm for bifurcation detection in vascular CTA scans

Endovascular imaging aims at identifying vessels and their branches. Automatic vessel segmentation and bifurcation detection eases both clinical research and routine work. In this article a state of the art bifurcation detection algorithm is developed and applied on vascular computed tomography angiography (CTA) scans to mark the common iliac artery and its branches, the internal and external iliacs. In contrast to other methods our algorithm does not rely on a complete segmentation of a vessel in the 3D volume, but evaluates the cross-sections of the vessel slice by slice. Candidates for vessels are obtained by thresholding, following by 2D connected component labeling and prefiltering by size and position. The remaining candidates are connected in a squared distanced weighted graph. With Dijkstra algorithm the graph is traversed to get candidates for the arteries. We use another set of features considering length and shape of the paths to determine the best candidate and detect the bifurcation. The method was tested on 119 datasets acquired with different CT scanners and varying protocols. Both easy to evaluate datasets with high resolution and no apparent clinical diseases and difficult ones with low resolution, major calcifications, stents or poor contrast between the vessel and surrounding tissue were included. The presented results are promising, in 75.7% of the cases the bifurcation was labeled correctly, and in 82.7% the common artery and one of its branches were assigned correctly. The computation time was on average 0.49 s ± 0.28 s, close to human interaction time, which makes the algorithm applicable for time-critical applications.

Vascular landmark detection in 3D CT data

This work presents novel methods to accurately placing landmarks inside the vessel lumen. This task is an important prerequisite to automatic centerline tracing. Methods have been proposed in the past to determine the location of organ landmarks, and yet several challenges remain for vascular landmarks. First, placing landmarks inside the lumen could be challenging for narrow vessels. Second, contrast-enhanced arteries could be tightly surrounded by bones with similar intensity profiles, making detection difficult compared to arteries surrounded only by darker tissues. Third, landmarks not located at bifurcations could be ill-defined as they have high uncertainty in position. We first present a method to detect landmarks that are located at vessel bifurcations. Such landmarks have well-defined positions, and we detect them using machine learning techniques. We then present a method to detect vascular landmarks not located at bifurcations. First, a segment detector is created to detect a vessel segment. Annotating multiple points along a vessel segment is easier than annotating a single landmark position, as there is no well-defined position along a vessel. This resolves the ambiguity issue mentioned above. Second, spatial features are computed from the segment detectors response map, and a regression model is created which takes as input the local spatial features surrounding a voxel, and outputs a confidence score of how likely this voxel is inside the lumen. We evaluate the system on a set of 94 3D CT datasets.

Statistical modeling of the arterial vascular tree

Automatic examination of medical images becomes increasingly important due to the rising amount of data. Therefore automated methods are required which combine anatomical knowledge and robust segmentation to examine the structure of interest. We propose a statistical model of the vascular tree based on vascular landmarks and unbranched vessel sections. An undirected graph provides anatomical topology, semantics, existing landmarks and attached vessel sections. The atlas was built using semi-automatically generated geometric models of various body regions ranging from carotid arteries to the lower legs. Geometric models contain vessel centerlines as well as orthogonal cross-sections in equidistant intervals with the vessel contour having the form of a polygon path. The geometric vascular model is supplemented by anatomical landmarks which are not necessarily related to the vascular system. These anatomical landmarks define point correspondences which are used for registration with a Thin-Plate-Spline interpolation. After the registration process, the models were merged to form the statistical model which can be mapped to unseen images based on a subset of anatomical landmarks. This approach provides probability distributions for the location of landmarks, vessel-specific geometric properties including shape, expected radii and branching points and vascular topology. The applications of this statistical model include model-based extraction of the vascular tree which greatly benefits from vessel-specific geometry description and variation ranges. Furthermore, the statistical model can be applied as a basis for computer aided diagnosis systems as indicator for pathologically deformed vessels and the interaction with the geometric model is significantly more user friendly for physicians through anatomical names.

Body landmark detection for a fully automatic AAA stent graft planning software system

In this paper, we present an approach to automate the planning of an endovascular stent graft for abdominal aortic aneurysms (AAAs), which are treated with bifurcated prosthesis (Y-stents) when located close to the iliac bifurcation. During the intervention, the folded Y-stent graft — consisting of several parts — is inserted via the iliac region and expanded inside the patients body. The first step of the proposed approach is to detect different body landmarks with a statistical method. In the next step, these landmarks are used to calculate two vascular centerlines, which provide multiplanar reformatting (MPR) slices that are used for an automatic segmentation of the artery walls. The segmented artery walls provide the manufacturer specific measures to choose an adequate bifurcated prosthesis. In a final step, the expansion of the stent is simulated in the patients data. Results for 50 abdominal aortic aneurysm cases provided by computed tomography angiography (CTA) acquisitions are successfully verified by a virtual stenting expert.