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Title: Left ventricle functional analysis in 2D+t contrast echocardiography within an atlas-based deformable template model framework
Author: Casero Cañas, Ramón
ISNI:       0000 0004 2676 0585
Awarding Body: University of Oxford
Current Institution: University of Oxford
Date of Award: 2008
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This biomedical engineering thesis explores the opportunities and challenges of 2D+t contrast echocardiography for left ventricle functional analysis, both clinically and within a computer vision atlas-based deformable template model framework. A database was created for the experiments in this thesis, with 21 studies of contrast Dobutamine Stress Echo, in all 4 principal planes. The database includes clinical variables, human expert hand-traced myocardial contours and visual scoring. First the problem is studied from a clinical perspective. Quantification of endocardial global and local function using standard measures shows expected values and agreement with human expert visual scoring, but the results are less reliable for myocardial thickening. Next, the problem of segmenting the endocardium with a computer is posed in a standard landmark and atlas-based deformable template model framework. The underlying assumption is that these models can emulate human experts in terms of integrating previous knowledge about the anatomy and physiology with three sources of information from the image: texture, geometry and kinetics. Probabilistic atlases of contrast echocardiography are computed, while noting from histograms at selected anatomical locations that modelling texture with just mean intensity values may be too naive. Intensity analysis together with the clinical results above suggest that lack of external boundary definition may preclude this imaging technique for appropriate measuring of myocardial thickening, while endocardial boundary definition is appropriate for evaluation of wall motion. Geometry is presented in a Principal Component Analysis (PCA) context, highlighting issues about Gaussianity, the correlation and covariance matrices with respect to physiology, and analysing different measures of dimensionality. A popular extension of deformable models ---Active Appearance Models (AAMs)--- is then studied in depth. Contrary to common wisdom, it is contended that using a PCA texture space instead of a fixed atlas is detrimental to segmentation, and that PCA models are not convenient for texture modelling. To integrate kinetics, a novel spatio-temporal model of cardiac contours is proposed. The new explicit model does not require frame interpolation, and it is compared to previous implicit models in terms of approximation error when the shape vector changes from frame to frame or remains constant throughout the cardiac cycle. Finally, the 2D+t atlas-based deformable model segmentation problem is formulated and solved with a gradient descent approach. Experiments using the similarity transformation suggest that segmentation of the whole cardiac volume outperforms segmentation of individual frames. A relatively new approach ---the inverse compositional algorithm--- is shown to decrease running times of the classic Lucas-Kanade algorithm by a factor of 20 to 25, to values that are within real-time processing reach.
Supervisor: Noble, J. Alison Sponsor: EPSRC ; Mirada Solutions Ltd ; Oriel College ; Department of Engineering Science (University of Oxford)
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: Life Sciences ; Bioinformatics (life sciences) ; Physiology and anatomy ; Biology and other natural sciences (mathematics) ; Mathematical biology ; Statistical mechanics,structure of matter (mathematics) ; Medical Sciences ; Anatomy ; Cardiovascular disease ; Mathematical genetics and bioinformatics (statistics) ; Bioinformatics (technology) ; Computing ; Applications and algorithms ; Engineering & allied sciences ; Biomedical engineering ; Information engineering ; Image understanding ; Mathematical modeling (engineering) ; Medical Engineering ; contrast ; echocardiography ; left ventricle ; functional analysis ; deformable template model ; Dobutamine Stress Echo ; endocardium ; global function ; local function ; visual scoring ; segmentation ; landmark ; texture ; geometry ; kinetics ; shape ; probabilistic atlas ; Power Modulation ; Principal Component Analysis ; Gaussianity ; correlation matrix ; covariance matrix ; dimensionality ; Active Appearance Model ; spatio-temporal model ; cardiac contours ; inverse compositional algorithm ; Lucas-Kanade ; gradient descent