Image databases in medical applications

The number of medical images acquired yearly in hospitals increases all the time. These imaging data contain lots of information on the characteristics of anatomical structures and on their variations. This information can be utilized in numerous medical applications. In deformable model-based segmentation and registration methods, the information in the image databases can be used to give a priori information on the shape of the object studied and the gray-level values in the image, and on their variations. On the other hand, by studying the variations of the object of interest in different populations, the effects of, for example, aging, gender, and diseases on anatomical structures can be detected. In the work described in this Thesis, methods that utilize image databases in medical applications were studied. Methods were developed and compared for deformable model-based segmentation and registration. Model selection procedure, mean models, and combination of classifiers were studied for the construction of a good a priori model. Statistical and probabilistic shape models were generated to constrain the deformations in segmentation and registration so that only the shapes typical to the object studied were accepted. In the shape analysis of the striatum, both volume and local shape changes were studied. The effects of aging and gender, and also the asymmetries were examined. The results proved that the segmentation and registration accuracy of deformable model-based methods can be improved by utilizing the information in image databases. The databases used were relatively small. Therefore, the statistical and probabilistic methods were not able to model all the population-specific variation. On the other hand, the simpler methods, the model selection procedure, mean models, and combination of classifiers, gave good results also with the small image databases. Two main applications were the reconstruction of 3-D geometry from incomplete data and the segmentation of heart ventricles and atria from short- and long-axis magnetic resonance images. In both applications, the methods studied provided promising results. The shape analysis of the striatum showed that the volume of the striatum decreases in aging. Also, the shape of the striatum changes locally. Asymmetries in the shape were found, too, but any gender-related local shape differences were not found.reviewe

Aspects on Cardiac Pumping

Cardiac pumping physiology is important for understanding the pathophysiology of patients with cardiac disease. MRI gives the opportunity to measure volumes and flow non-invasively with high accuracy and precision. This thesis examines some aspects on cardiac pumping physiology. Study I showed that the total heart volume in humans decreases during systole by ~8 % (range 5-11 %), and anatomically identified the major outer volume variations to occur around the AV-plane with a left-side predominance. Also, a new method for measuring total heart volume variation (THVV) by MRI flow quantification was developed and validated against cine measurements. Study II showed that the THVV is similar in patients before and after cardiac bypass surgery compared to healthy subjects. Furthermore, study II also showed that the movement of the center of volume of the heart during the cardiac cycle, in both healthy individuals and patients, describes a well-defined loop in three-dimensional space with ~2 mm between the extreme points. This loop is called the center of volume variation, COVV. After coronary-bypass surgery, however, intra-individual COVV approximately doubled, possibly related to the paradoxical septal movement following cardiac surgery. Study III showed that longitudinal AV-plane displacement (AVPD) is the primary contributor to left ventricular (LV) pumping, accounting for ~60 % of the stroke volume (SV) in healthy subjects and that this does not differ in athletes or in patients with dilated ventricles. Study IV showed that radial function of the ventricles explains over 80 % of the THVV during the cardiac cycle. The longitudinal component of right ventricular (RV) pumping is ~80 % and the difference compared to the LV is explained by the larger AVPD of the RV. Study V identified and quantified a previously unknown increase in total heart volume before the end of systolic ejection. This total heart volume increase or late ejection filling volume (LEFV) into the atria was ~11 ml or ~18 % of THVV, with no difference between the left and right side of the heart. This volume might be important for understanding the coupling of systolic to diastolic function. Furthermore, the decrease in total heart volume caused by flow from the heart generated by atrial contraction (the atrial wave reversal volume, AWRV) was quantified to be ~7 ml or ~11 % of THVV. Thus, the heart is largest before atrial contraction prior to the end of diastole and smallest before the end of systole. In summary, this thesis has explained the total heart volume variations throughout the cardiac cycle and quantified the contribution of the AV-plane to ventricular pumping

QUANTIFICATION OF MYOCARDIAL MECHANICS IN LEFT VENTRICLES UNDER INOTROPIC STIMULATION AND IN HEALTHY RIGHT VENTRICLES USING 3D DENSE CMR

Statistical data from clinical studies indicate that the death rate caused by heart disease has decreased due to an increased use of evidence-based medical therapies. This includes the use of magnetic resonance imaging (MRI), which is one of the most common non-invasive approaches in evidence-based health care research. In the current work, I present 3D Lagrangian strains and torsion in the left ventricle of healthy and isoproterenol-stimulated rats, which were investigated using Displacement ENcoding with Stimulated Echoes (DENSE) cardiac magnetic resonance (CMR) imaging. With the implementation of the 12-segment model, a detailed profile of regional cardiac mechanics was reconstructed for each subject. Statistical analysis revealed that isoproterenol induced a significant change in the strains and torsion in certain regions at the mid-ventricle level. In addition, I investigated right ventricular cardiac mechanics with the methodologies developed for the left ventricle. This included a comparison of different regions within the basal and mid-ventricular regions. Despite no regional variation found in the peak circumferential strain, the peak longitudinal strain exhibited regional variation at the anterior side of the RV due to the differences in biventricular torsion, mechanism of RV free wall contraction, and fiber architecture at RV insertions. Future applications of the experimental work presented here include the construction and validation of biventricular finite element models. Specifically, the strains predicted by the models will be statistically compared with experimental strains. In addition, the results of the present study provide an essential reference of RV baseline evaluated with DENSE MRI, a highly objective technique

Evaluation of left ventricle strains by applying SPAMM cardiac MRI techniques

Tese de mestrado integrado em Engenharia Biomédica e Biofísica, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2017As doenças cardiovasculares são uma das maiores causas de morte no mundo, causando aproximadamente 17.5 milhões de mortes por ano, o que corresponde a 31% de todas as mortes no mundo. Estas doenças caracterizam-se pela diminuição da contração da parede do miocárdio durante o ciclo cardíaco. Uma das doenças mais comuns é a cardiomiopatia dilatada (DCM), onde o músculo cardíaco fica mais fino e fraco, e as cavidades cardíacas ficam aumentadas. Consequentemente, a capacidade de deformação do miocárdio é diminuída, o que impossibilita o coração de bombear eficientemente o sangue para as restantes partes do corpo. Esta condição é maioritariamente genética, mas também pode ser provocada por diferentes causas como infeções virais, inflamações ou lesões. A análise da deformação da parede do miocárdio aquando do ciclo cardíaco possibilita não só a identificação das deformações normais do miocárdio aquando da sua contração, mas também das deformações anormais devido a doenças cardíacas. A técnica de ressonância magnética cardíaca (CMR) é não invasiva e tem uma elevada resolução espacial, sendo por isso indispensável no estudo destas deformações. Esta técnica permite detetar essas mesmas características da contração e distensão do músculo cardíaco, possibilitando a análise das deformações e a respetiva distinção entre os pacientes saudáveis e os pacientes com cardiomiopatia dilatada. Nesta doença, observa-se o estreitamento das paredes do miocárdio e a dilatação das cavidades cardíacas, como é o caso do ventrículo esquerdo, o que se observa pelo aumento do seu diâmetro. O resultado é um decréscimo significativo na tensão e deformação da parede do miocárdio, o que impacta negativamente na eficiência da sístole ventricular. A técnica de Modulação Espacial da Magnetização (SPAMM) tem vindo a ser proposta para a visualização do movimento e deslocamento da parede do miocárdio no seu plano de imagem, através da criação de padrões de linhas e grelhas com magnetização alterada na imagem. Estes padrões são marcadores que seguem a deformação do músculo cardíaco. Ao serem detetados e seguidos durante o ciclo cardíaco, estes marcadores contribuem para o estudo do movimento da parede do miocárdio aquando da sua contração. A amostra usada nesta tese consistiu em imagens de ressonância magnética cardíaca de 9 indivíduos, 3 dos quais são saudáveis e os outros 6 são pacientes com DCM. As imagens foram adquiridas pelo Hospital Motol em Praga (República Checa) e analisadas pelo Instituto de Informática, Robótica and Cibernética da Faculdade de Engenharia Elétrica em Praga. A tese proposta teve como objetivo o estudo da deformação radial no ventrículo esquerdo através da automatização na deteção dos marcadores presentes no mesmo, assim como no seu seguimento ao longo do ciclo cardíaco. Pela análise das deformações de voluntários saudáveis e de pacientes com cardiomiopatia dilatada, é possível comparar os seus padrões de deformação cardíaca de modo a analisar as diferenças entre os dois. Pelo estudo das deformações, sabe-se que um valor positivo de deformação corresponde a um espessamento de um objeto e um valor negativo corresponde ao seu encurtamento, relativamente ao seu tamanho inicial. Durante a contração do miocárdio, é normal observar-se um espessamento e encurtamento da parede do ventrículo esquerdo. Assim sendo, as deformações radiais tomam valores positivos devido ao espessamento da parede e as circunferenciais tomam valores negativos devido ao encurtamento da parede. Os métodos de deteção dos marcadores foram aplicados com sucesso nos sujeitos saudáveis e com cardiomiopatia dilatada, sendo que estes marcadores foram também corretamente seguidos ao longo do ciclo cardíaco, durante a sístole e a diástole. Nos sujeitos saudáveis, foi observado um intervalo de deformações radiais entre 18.63 % e 43.84 %, enquanto que em pacientes com cardiomiopatia dilatada, os valores de deformação radial variaram entre 10.73 % e 14.14 %. De notar que os valores das deformações radiais são positivos e, por isso, confirmam o espessamento da parede do ventrículo esquerdo aquando da sua contração. Assim sendo, os resultados desta dissertação vão de encontro com os resultados dos testes feitos anteriormente em voluntários saudáveis e com cardiomiopatia dilatada, visto que os intervalos de deformações são semelhantes para os dois grupos. Ao comparar-se as deformações dos dois grupos pelo teste estatístico Mann-Whitney, verificou-se uma diferença significativa (p<0.05) nos valores das deformações entre os mesmos. Assim sendo, esta tese também confirma que os pacientes com a doença cardíaca têm valores mais baixos de deformação em relação aos indivíduos saudáveis, tal como é comprovado pelo facto da doença cardiomiopatia dilatada ser caracterizada pela diminuição da deformação do miocárdio durante o ciclo cardíaco. Pela comparação dos diferentes segmentos ao longo das secções básica, média e apical do ventrículo esquerdo, foi também observado que nos pacientes com cardiomiopatia dilatada, a deformação mínima correspondeu ao segmento inferolateral da base do ventrículo e que a deformação máxima se deu no segmento anteroseptal da secção média do ventrículo. Em contrapartida, nos indivíduos saudáveis, o mínimo da deformação foi no segmento anterior e o máximo da deformação correspondeu ao segmento inferoseptal, ambos os segmentos pertencentes à secção média do ventrículo esquerdo. Estes resultados foram também observados em estudos anteriores relativos a pacientes com cardiomiopatia dilatada. Relativamente à análise das deformações circunferenciais, foi observado que, nos sujeitos saudáveis, o intervalo das deformações esteve entre -32.17 % e -24.33 %, enquanto que nos pacientes com cardiomiopatia dilatada, o intervalo foi de -15.92 % a -8.17 %. O valor negativo da deformação circunferencial é devido ao encurtamento da parede do ventrículo esquerdo, sendo que este valor se encontra em conformidade com o correto comportamento da parede do ventrículo durante a contração do miocárdio, tal como observado em estudos anteriores. Para alem destes factos, também se verificou que o máximo da deformação circunferencial foi dado na secção media do ventrículo esquerdo, enquanto que o mínimo foi na secção apical do mesmo. Ao comparar-se as deformações circunferenciais, pelo teste estatístico Mann-Whitney, durante a systole e entre os dois grupos de sujeitos, verificou-se existe uma diminuição significativa (p<0.05) do seu valor absoluto nos pacientes, relativamente aos sujeitos saudáveis. Adicionalmente, também foi estudado o efeito do género (masculino / feminino) nas deformações dos pacientes com cardiomiopatia dilatada. Os resultados do estudo mostraram que as deformações do ventrículo esquerdo são maiores no género masculino, em relação ao género feminino. Contudo, outros estudos realizados anteriormente não relataram qualquer relação entre as deformações do miocárdio e o género (masculino / feminino) dos respetivos pacientes. Com esta dissertação foi possível concluir que o estudo das deformações no ventrículo esquerdo é um parâmetro importante na avaliação da contratilidade do coração. O facto de a Ressonância magnética ser uma técnica não invasiva e da técnica de Modulação espacial da magnetização permitir criar um padrão de grelha que facilmente acompanha movimentos na parede do músculo, possibilitou a eficiente deteção das deformações na parede do ventrículo esquerdo. Uma outra conclusão importante deste estudo é o facto da doença cardiomiopatia dilatada provocar uma diminuição da capacidade de deformação do coração, visto que a doença é caracterizada pelo estreitamento da parede do miocardio e por uma dilatação das cavidades cardíacas, especialmente dos ventrículos. Este facto está na origem da diminuição das deformações radiais e circunferenciais, em relação às deformações dos pacientes saudáveis. Foi também observado que a secção do ventrículo esquerdo responsável pela maior deformação é a secção média, pois foi nesta secção que se observou um maior número de valores máximos de deformação. Por fim, nesta tese também se confirma que durante a contração do miocárdio, a deformação radial teve valores positivos e a deformação circunferencial teve valores negativos, o que comprova que houve um espessamento e encurtamento da parede do ventrículo esquerdo durante a sua contração. Assim sendo, verifica-se que ao longo desta dissertação foi possível analisar a relação da deformação do ventrículo esquerdo com a doença cardiomiopatia dilatada e consequentemente, avaliar se a deformação calculada é normal ou devido à doença cardíaca. Como tal, a partir deste estudo foi possível facilitar a deteção das deformações, bem como fazer a sua análise para contribuição do estudo das doenças cardíacas, tal como a cardiomiopatia dilatada. Como trabalho futuro, poderá estudar-se como detetar automaticamente o ventrículo esquerdo e como calcular eficientemente as suas deformações. Assim, poderá também aprofundar-se o estudo e a análise da doença cardiomiopatia dilatada e de outras doenças cardíacas.Cardiovascular diseases are one of the main causes of death in the world. These diseases modify the myocardial wall contraction during cardiac cycle. One of the most common types of these diseases is the dilated cardiomyopathy (DCM), in which the heart muscle becomes weaker and the heart cavities are enlarged. Consequently, the heart deformation capability is decreased, which prevents it from pumping blood efficiently. This condition can be genetic or due to various causes such as viral infections, inflammation or injuries. The analysis of cardiac wall deformation enables identifying normal or abnormal deformations due to heart disease. Cardiac Magnetic Resonance Imaging (MRI) is able to detect the characteristic abnormalities of DCM, which are the wall thinning and dilation of heart chambers, more specifically the increasing of ventricle diameter. The result is a significant decrease in wall stress and strain, which has a negative impact on systolic ventricular performance. The Spatial Modulation of Magnetization (SPAMM) technique has been proposed for imaging myocardial motion within the plane of the image by creating a pattern of lines or grids with altered magnetization on the image. These patterns are tags that deform according to the heart muscle deformation and can be detected and tracked for wall motion studying. The sample used in this thesis was composed by cardiac MRI scans of 9 subjects, 3 of which were healthy subjects and the other 6 were patients with DCM. The scans were acquired by Motol Hospital in Prague (Czech Republic) and analyzed in the Institute of Informatics, Robotics and Cybernetics from the Faculty of Electrical Engineering in Prague. The proposed thesis intended to assess the left ventricle (LV) radial and circumferential strains by automatically detecting LV tags and tracking those during cardiac cycle. By analyzing the heart strains from healthy subjects and patients with DCM, it is possible to compare both patterns of cardiac deformation within the cardiac cycle in order to analyze the differences between them. Positive strain values describe myocardial thickening and negative values describe its shortening, related to its original length. During myocardial contraction, the radial strain is positive due to myocardial thickening, and the circumferential strain is negative due to myocardial shortening. The tracking methods were successfully applied on heathy and DCM patients and the tags were successfully detected during systole and diastole. A comparison between the strains, by Mann-Whitney statistical test, during the cardiac cycle in both sets of subjects, identified a significant difference (p<0.05) between them. It was observed that in healthy subjects, the radial strain varied from 18.63 % to 43.84 %, while in DCM patients, the radial strain varied from 10.73 % to 14.14 %. The radial strains are positive values, as the LV thickens during myocardial contraction. The results of this thesis are in agreement with previous studies done with DCM and healthy subjects, as the ranges of deformations are similar in both sets of subjects. Moreover, this thesis also confirms that DCM patients have lower radial strain values than healthy subjects, as DCM is characterized by a decrease in heart muscle strain during the cardiac cycle. By comparing several segments in the different sections of the heart, it was also observed that in DCM patients, the minimum deformation was on the inferolateral segment of the base, while the maximum was on the anteroseptal segment of the middle section. However, in healthy subjects, the minimum deformation was on the anterior segment and the maximum was on the inferoseptal segment, both in the middle section of the left ventricle. This result was also observed in previous studies. Regarding to the circumferential strains analysis, it was observed that in healthy subjects, the average circumferential strain range was from -32.17 % to -24.33 %, while in DCM patients, it was from -15.92 % to -8.17 %. The negative value of the circumferential strain means that there was a LV wall shortening and this is in conformity with the correct behavior of LV during myocardial contraction. Moreover, in healthy subjects, the mid section of LV has the major strain, while in DCM patients, it is the apical section. A comparison between the circumferential strains during systole in both sets of subjects supports the previous studies results, in which the circumferential stains values are negative during systole. Additionally, the results of Mann-Whitney statistical test also shown significant lower absolute (p<0.05) values on DCM patients, when comparing to healthy subjects. Additionally, the effect of the gender (male/ female) on the strains was also investigated on the DCM patients and the results suggest that in women, the LV strain is lower than in men. Despite these results, the other studies did not report any conclusion related to this effect. It is possible to state that the study of the LV strain is an important parameter in the evaluation of the cardiac contractility. A non-invasive assessment of LV by MRI and the superimposed grid created by SPAMM improved the tracking of LV wall strains. Another important conclusion of this study was that DCM decreases the deformation capabilities of the heart, as it is responsible for the wall thinning and dilation of heart chambers, causing a decrease in wall radial and circumferential strains. Moreover, it was observed that the major section responsible for the myocardial deformation was the middle section of the LV. Finally, this thesis also confirmed that during myocardial contraction, the radial strain values are positive due to the myocardial thickening and the circumferential values are negative due to the myocardial shortening. A need to automatically detect the LV and also to efficiently calculate the LV strains in a short time can be developed as a future work, which will also improve the analysis of DCM disease and other cardiac diseases

Foetal echocardiographic segmentation

Congenital heart disease affects just under one percentage of all live births [1]. Those defects that manifest themselves as changes to the cardiac chamber volumes are the motivation for the research presented in this thesis. Blood volume measurements in vivo require delineation of the cardiac chambers and manual tracing of foetal cardiac chambers is very time consuming and operator dependent. This thesis presents a multi region based level set snake deformable model applied in both 2D and 3D which can automatically adapt to some extent towards ultrasound noise such as attenuation, speckle and partial occlusion artefacts. The algorithm presented is named Mumford Shah Sarti Collision Detection (MSSCD). The level set methods presented in this thesis have an optional shape prior term for constraining the segmentation by a template registered to the image in the presence of shadowing and heavy noise. When applied to real data in the absence of the template the MSSCD algorithm is initialised from seed primitives placed at the centre of each cardiac chamber. The voxel statistics inside the chamber is determined before evolution. The MSSCD stops at open boundaries between two chambers as the two approaching level set fronts meet. This has significance when determining volumes for all cardiac compartments since cardiac indices assume that each chamber is treated in isolation. Comparison of the segmentation results from the implemented snakes including a previous level set method in the foetal cardiac literature show that in both 2D and 3D on both real and synthetic data, the MSSCD formulation is better suited to these types of data. All the algorithms tested in this thesis are within 2mm error to manually traced segmentation of the foetal cardiac datasets. This corresponds to less than 10% of the length of a foetal heart. In addition to comparison with manual tracings all the amorphous deformable model segmentations in this thesis are validated using a physical phantom. The volume estimation of the phantom by the MSSCD segmentation is to within 13% of the physically determined volume

A dynamic 3-D cardiac surface model from MR images

Cardiac 3D + time segmentation and motion estimation are recognized as difficult prerequisite tasks for any quan-titative analysis of cardiac images. Some recent algorithms aim to consider a temporal constraint to increase the ac-curacy of results. To improve the temporal consistency, prior knowledge about cardiac dynamics can be used. In this paper, we propose to build a new Statistical Dynamic Model (SDM) of the heart by learning through a popula-tion of healthy individuals. This SDM is composed by a set of semi-landmarks which describe the heart surfaces. For each of them, a mean trajectory and variability around it are derived. The SDM provides a reasonable constraint for a temporally regularized segmentation and motion track-ing algorithm. 1

BIVENTRICULAR FINITE ELEMENT MODELING AND QUANTIFICATION OF 3D LANGRAGIAN STRAINS AND TORSION USING DENSE MRI

Statistical data suggests that increased use of evidence-based medical therapies has largely contributed to the decrease in American death rate caused by heart disease. And my studies are about two applications of magnetic resonance imaging (MRI) as a non-invasive approach in evidence-based health care research. In my first study, the achievement of a pulmonary valve replacement surgery was assessed on a patient with tetralogy of Fallot (TOF). In order to evaluate the remodeling of right ventricle, two biventricular finite element models were built up for pre-surgical images and post-surgical images. In my second study, 3D Lagrangian strains and torsion in the left ventricle of ten rats were investigated using Displacement ENcoding with Stimulated Echoes (DENSE) cardiac magnetic resonance (CMR) images. Tools written in MATLAB were developed for 2D contouring, 3D modeling, strain and torsion computations, and statistical comparison across subjects