Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Fully automated segmentation and tracking of the intima media thickness in ultrasound video sequences of the common carotid artery

Abstract—The robust identification and measurement of the intima media thickness (IMT) has a high clinical relevance because it represents one of the most precise predictors used in the assessment of potential future cardiovascular events. To facilitate the analysis of arterial wall thickening in serial clinical investigations, in this paper we have developed a novel fully automatic algorithm for the segmentation, measurement, and tracking of the intima media complex (IMC) in B-mode ultrasound video sequences. The proposed algorithm entails a two-stage image analysis process that initially addresses the segmentation of the IMC in the first frame of the ultrasound video sequence using a model-based approach; in the second step, a novel customized tracking procedure is applied to robustly detect the IMC in the subsequent frames. For the video tracking procedure, we introduce a spatially coherent algorithm called adaptive normalized correlation that prevents the tracking process from converging to wrong arterial interfaces. This represents the main contribution of this paper and was developed to deal with inconsistencies in the appearance of the IMC over the cardiac cycle. The quantitative evaluation has been carried out on 40 ultrasound video sequences of the common carotid artery (CCA) by comparing the results returned by the developed algorithm with respect to ground truth data that has been manually annotated by clinical experts. The measured IMTmean ± standard deviation recorded by the proposed algorithm is 0.60 mm ± 0.10, with a mean coefficient of variation (CV) of 2.05%, whereas the corresponding result obtained for the manually annotated ground truth data is 0.60 mm ± 0.11 with a mean CV equal to 5.60%. The numerical results reported in this paper indicate that the proposed algorithm is able to correctly segment and track the IMC in ultrasound CCA video sequences, and we were encouraged by the stability of our technique when applied to data captured under different imaging conditions. Future clinical studies will focus on the evaluation of patients that are affected by advanced cardiovascular conditions such as focal thickening and arterial plaques

Identification of weakly coupled multiphysics problems. Application to the inverse problem of electrocardiography

This work addresses the inverse problem of electrocardiography from a new perspective, by combining electrical and mechanical measurements. Our strategy relies on the defini-tion of a model of the electromechanical contraction which is registered on ECG data but also on measured mechanical displacements of the heart tissue typically extracted from medical images. In this respect, we establish in this work the convergence of a sequential estimator which combines for such coupled problems various state of the art sequential data assimilation methods in a unified consistent and efficient framework. Indeed we ag-gregate a Luenberger observer for the mechanical state and a Reduced Order Unscented Kalman Filter applied on the parameters to be identified and a POD projection of the electrical state. Then using synthetic data we show the benefits of our approach for the estimation of the electrical state of the ventricles along the heart beat compared with more classical strategies which only consider an electrophysiological model with ECG measurements. Our numerical results actually show that the mechanical measurements improve the identifiability of the electrical problem allowing to reconstruct the electrical state of the coupled system more precisely. Therefore, this work is intended to be a first proof of concept, with theoretical justifications and numerical investigations, of the ad-vantage of using available multi-modal observations for the estimation and identification of an electromechanical model of the heart

Automatic multiscale vascular image segmentation algorithm for coronary angiography

[Abstract] Cardiovascular diseases, particularly severe stenosis, are the main cause of death in the western world. The primary method of diagnosis, considered to be the standard in the detection and quantification of stenotic lesions, is a coronary angiography. This article proposes a new automatic multiscale segmentation algorithm for the study of coronary trees that offers results comparable to the best existing semi-automatic method. According to the state-of-the-art, a representative number of coronary angiography images that ensures the generalisation capacity of the algorithm has been used. All these images were selected by clinics from an Haemodynamics Unit. An exhaustive statistical analysis was performed in terms of sensitivity, specificity and Jaccard. Algorithm improvements imply that the clinician can perform tests on the patient and, bypassing the images through the system, can verify, in that moment, the intervention of existing differences in a coronary tree from a previous test, in such a way that it could change its clinical intra-intervention criteria.Galicia. Consellería de Cultura, Educación e Ordenación Universitaria; GRC2014/049Ministerio de Economía y Competitividad; TIN2015-70648-

TMA Vessel Segmentation Based on Color and Morphological Features: Application to Angiogenesis Research

Given that angiogenesis and lymphangiogenesis are strongly related to prognosis in neoplastic and other pathologies and that many methods exist that provide different results, we aim to construct a morphometric tool allowing us to measure different aspects of the shape and size of vascular vessels in a complete and accurate way. The developed tool presented is based on vessel closing which is an essential property to properly characterize the size and the shape of vascular and lymphatic vessels. The method is fast and accurate improving existing tools for angiogenesis analysis. The tool also improves the accuracy of vascular density measurements, since the set of endothelial cells forming a vessel is considered as a single object

Deep Learning in Cardiology

The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table

MR image based measurement, modelling and diagnostic interpretation of pressure and flow in the pulmonary arteries: applications in pulmonary hypertension

Pulmonary hypertension (PH) is a clinical condition characterised by an increased mean pulmonary arterial pressure (mPAP) of over 25 mmHg measured, at rest, by right heart catheterisation (RHC). RHC is currently considered the gold standard for diagnosis, follow-up and measurement of response to treatment. Although the severe complications and mortality risk associated with the invasive procedure are reduced when it is performed in a specialist centre, finding non-invasive PH diagnosis methods is highly desirable. Non-invasive, non-ionising imaging techniques, based on magnetic resonance imaging (MRI) and on echocardiography, have been integrated into the clinical routine as means for PH assessment. Although the imaging techniques can provide valuable information supporting the PH diagnosis, accurately identifying patients with PH based upon images alone remains challenging. Computationally based models can bring additional insights into the haemodynamic changes occurring under the manifestation of PH. The primary hypothesis of this thesis is that that the physiological status of the pulmonary circulation can be inferred using solely non-invasive flow and anatomy measurements of the pulmonary arteries, measured by MRI and interpreted by 0D and 1D mathematical models. The aim was to implement a series of simple mathematical models, taking the inputs from MRI measurements, and to evaluate their potential to support the non-invasive diagnosis and monitoring of PH. The principal objective was to develop a tool that can readily be translated into the clinic, requiring minimum operator input and time and returning meaningful and accurate results. Two mathematical models, a 3 element Windkessel model and a 1D model of an axisymmetric straight elastic tube for wave reflections were implemented and clinically tested on a cohort of healthy volunteers and of patients who were clinically investigated for PH. The latter group contained some who were normotensive, and those with PH were stratified according to severity. A 2D semi-automatic image segmentation workflow was developed to provide patient specific, simultaneous flow and anatomy measurements of the main pulmonary artery (MPA) as input to the mathematical models. Several diagnostic indices are proposed, and of these distal resistance (Rd), total vascular compliance (C) and the ratio of reflected to total wave power (Wb/Wtot) showed statistically significant differences between the analysed groups, with good accuracy in PH classification. A machine learning classifier using the derived computational metrics and several other PH metrics computed from MRI images of the MPA and of the right ventricle alone, proposed in the literature as PH surrogate markers, was trained and validated with leave-one-out cross-validation to improve the accuracy of non-invasive PH diagnosis. The results accurately classified 92% of the patients, and furthermore the misclassified 8% were patients with mPAP close to the 25 mmHg (at RHC) threshold (within the range of clinical uncertainty). The individual analysis of all PH surrogate markers emphasised that wave reflection quantification, although with lower diagnosis accuracy (75%) than the machine learning model embedding multiple markers, has the potential to distinguish between multiple PH categories. A finite element method (FEM) based model to solve a 1D pulmonary arterial tree linear system, has been implemented to contribute further to the accurate, non-invasive assessment of pulmonary hypertension. The diagnostic protocols, including the analysis work flow, developed and reported in this PhD thesis can be integrated into the clinical process, with the potential to reduce the need for RHC by maximising the use of available MRI data