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Comparison of the preclinical DCE-MRI perfusion techniques
Minsterová, Alžběta ; Jiřík, Radovan (referee) ; Macíček, Ondřej (advisor)
This diploma thesis deals with DCE-MRI (Dynamic Contrast-Enhanced Magnetic Resonance Imaging) thus one of the contrast magnetic resonance imaging methods. It describes the principle of conventional continuous DCE-MRI, which uses single bolus of contrast agent and further it focuses on the dual bolus contrast agent techniques, especially the interleaved acquisition. The graphical interface for processing Bruker systems data was made. Synthetic data were used to evaluate the influence of this method on the perfusion parameters estimation. Simulations proved that the further the second bolus is from the first one, the better results are. Simulations of acquisition interruption did not lead to the clear result. However, two statements, which are expected to lead to as good estimation of perfusion parameters as possible, were formulated
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Calculation of advanced diffusion parameters in brain grey matter from DKI MRI images
Pánková, Olga ; Jakubíček, Roman (referee) ; Minsterová, Alžběta (advisor)
Thesis named Calculation of advanced diffusion parameters in brain grey matter from DKI MRI images deals with processing of diffusion-weighted images from DKI. The thesis contains review of literature on principle of diffusion, influence of diffusion on MRI, calculation of DTI and DKI parameters and clinical application of diffusion-weighted maps with focus on grey matter. The thesis focuses on software tools for processing and pre-processing DTI and DKI. The practical part consisted of two sections. Two different softwares were used to calculate maps of diffusion parameters. Diffusion parameters from anatomical structure sunstantia nigra were compared between group of healthy controls and patients with Parkinson’s disease. This comparison did not show any statisticaly significant difference. In the second step, a script for creating diffusion maps in software Diffusinal Kurtosis Estimator was made.
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Segmentation of cardiac tissue fibrosis in MRI data
Sokol, Norbert ; Mézl, Martin (referee) ; Kolář, Radim (advisor)
Late gadolinium enhancement cardiovascular magnetic resonance imaging can be used to visualize pre-ablation fibrosis or post-ablation myocardial scar. This can significantly helps physicians with diagnosis patients who suffer from myocardial fibrosis to determine region of fibrosis and for post-operative validation of intervention after radio-frequency catheter ablation. In this thesis, i introduce an algorithm for successful distinguish of fibrosis on datasets of patients with myocardial fibrosis, scanned at Faculty hospital at St. Anne’s University Hospital.
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MRI Acquisition and Preprocessing of Image Sequences for Clinical Perfusion Imaging
Krchňavý, Jan ; Bartoš, Michal (referee) ; Jiřík, Radovan (advisor)
This thesis describes the theory for static and dynamic magnetic-resonance imaging using contrast agents affecting T1 relaxation time. The available acquisition methods in the specified facility of Masaryk Oncological Institute in Brno are described. The sequences for subsequent experimental measurements are selected. The used phantoms are described. Acquisition protocol for measuring is described briefly and the evaluation method for the measured data is suggested. The best acquisition sequence and a method of measurements is chosen influenced by estimation of relaxation time T1, sensitivity and signal to noise ratio. Perfusion analysis is executed and perfusion parameters are calculated. The work was supported by the European Regional Development Fund and the State Budget of the Czech Republic (RECAMO, CZ.1.05/2.1.00/03.0101).
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Image segmentation of spinal disc in medical imaging
Meloun, Jan ; Nemček, Jakub (referee) ; Mézl, Martin (advisor)
This thesis is focused on segmentation of intervertebral discs in images from two medical imaging modalities - computed tomography (CT) and magnetic resonance imaging (MRI). Theoretical introduction of the thesis describes intervertebral disc herniation and relevant imaging modalities. It also includes description of basic and advanced segmentation methods. For practical part of the thesis, three different segmentation teqniques (one for CT data and two for MRI images) have been chosen, implemented and applied on images acquired at Radiodiagnostic department of Havlíčkův Brod hospital. The segmentation quality has been assessed quantitatively for individual methods by comparing the segmentation results to manually created reference segmentation of intervertebral discs.
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Multiparametric segmentation of MR images
Chovanec, Ján ; Šmirg, Ondřej (referee) ; Dvořák, Pavel (advisor)
The aim of the thesis was familiarity of segmentation methods for automatic segmentation of MR images, using multiparametrical display. The theoretical part focuses on the description of methods of segmentation techniques. In the practical part are implemented K-means and level-set method. The methods are tested on the images of the brain obtained by different sequences (T1, T1c, T2, FLAIR). Segmentation methods are implemented in the program MATLAB. Implemented segmentation accuracy is demonstrated on data which there are reports reference results. Evaluation methods is performed using different classifiers decision. The K-means method is tested different metrics and different combinations of the input image. Finally, both methods are compared with one another and visually evaluated against the reference image.
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Correlates finding of heart rate changes in fMRI data
Jurečková, Kateřina ; Gajdoš, Martin (referee) ; Bartoň, Marek (advisor)
This master’s thesis deals with problematic of correlates finding of heart rate changes in fMRI data. The first part describes principle of fMRI, creation of BOLD signal, data acquisition, their pre-processing and analysis. The next part describes heart rate variability and its impact on fMRI data. The following section is dedicated to pre-processing of heart rate time series to the form, which can be used in correlates finding of heart rate variability and fMRI data with generalized linear model. The process of statistical testing and its result with discussion can be found in the last part of this thesis.
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Analysis of Selected Artefacts in Diffusion-Based Magnetic Resonance Measurements
Marcoň, Petr ; Král, Bohumil (referee) ; Frollo, Ivan (referee) ; Bartušek, Karel (advisor)
The presented dissertation thesis analyses artefacts in diffusion-weighted images. In medical practice, the artefacts can impede the diagnostics of pathological tissues and, therefore, need to be eliminated. As the first step within the thesis, an analysis of the most frequent artefacts in diffusion-weighted images is performed, and the hitherto known approaches to artefact elimination are described. In order to facilitate the reduction of artefacts caused by the inhomogeneity of the static magnetic field and induced by eddy currents, a novel three-measurement method is shown. This technique will find application especially in measuring the diffusion coefficient of isotropic materials. At this point, it is important to note that a significant and commonly found problem is the magnetic susceptibility artefact; different magnetic susceptibility values at the boundary between two materials can cause magnetic field inhomogeneities and even complete loss of the signal. Therefore, we designed a novel method for the measurement of magnetic susceptibility in various samples of magnetically incompatible materials, which do not produce any MR signal. The technique was experimentally verified using a set of differently shaped diamagnetic and paramagnetic samples. In addition to the magnetic susceptibility problem, the thesis presents artefacts such as noise, motion-induced items, hardware limitations, chemical shift, and the dependence of the diffusion coefficient on the temperature. To enable precise measurement of the diffusion coefficient, we proposed a thermal system; in the experiment, it was determined that when the measurement error does not exceed 5%, the temperature change should not be higher than 0,1 °C. In the final sections of the thesis, practical application examples involving the designed methods are shown.
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Implementation of Dixon Methods for Preclinical MR Imaging at High Fields
Kořínek, Radim ; Latta,, Peter (referee) ; Puková,, Andrea Šprláková - (referee) ; Bartušek, Karel (advisor)
Preklinické magneticko-rezonanční (MR) zobrazování na malých zvířatech je velmi aktuální a vyžaduje, vzhledem k rozměrům těchto zvířat, vyšší citlivost. Vyšší citlivosti lze dosáhnout použitím MR systému s vysokým základním magnetickým polem (např. 4,7 T a výše). Vyšší citlivost přináší výhody v podobě možnosti vyššího rozlišení, lepší poměr signál-šum, větší chemický posuv, prodloužení longitudinální relaxace (T1), atd. Na druhou stranu vyšší magnetické pole znamená větší deformace základního magnetického pole na rozhraních tkání s rozdílnou susceptibilitou a zkrácení transverzální relaxace (T2). Tuková tkáň je významně zastoupena v lidském těle a primárně sloužící pro uchovávání energie ve formě tuků. Tukovou tkáň lze rozdělit na hnědou a bílou tukovou tkáň. Hnědá tuková tkáň se vyskytuje hlavně u novorozenců, ale může být ve velmi malém množství také u dospělých jedinců. Bílá tuková tkáň je určena pro ukládání tuků, které slouží jako zdroj energie. Kromě toho bílá tuková tkáň produkuje adipokiny, hormony a mnoho dalších látek důležitých pro náš metabolizmus. Tuk lze obecně považovat jako biomarker při určitých nemocech (obezita, steatóza jater, a další). Z tohoto důvodu je kvantifikace tuku velmi důležitá pro správnou diagnózu. V MR zobrazování je speciální skupina metod pro separaci vody a tuku. Tyto metody se nazývají Dixonovy metody a jejich princip je založen na chemickém posuvu. V této práci je popsána nová T2-váhovaná sekvence pro Dixonovu akvizici (Kapitola 5.3). Navržená sekvence je z hlediska akviziční doby velmi efektivní a řadí se mezi tříbodové Dixonovy (3PD) techniky. Nově navržená sekvence fast triple spin echo Dixon (FTSED) vychází z původní sekvence rychlého spinového echa (FSE). Modifikací původní sekvence FSE vedla ke vzniku nové sekvence FTSED, která umožňuje získat tři obrazy během jediné akvizice, bez toho aniž bychom prodloužili celkovou dobu měření. Sekvence byla úspěšně implementována na 9,4 T MRI systém na Ústavu přístrojové techniky v Brně. Získaná data byla pak zpracována iterativně pomocí algoritmu IDEAL (iterative decomposition of water and fat with echo asymmetry and least-squares estimation). Výsledkem jsou separátní obrazy vody a tuků, z kterých lze vypočítat mapy frakce tuku (FF-mapy). Sekvence byla ověřena na fantomech a poté byla odzkoušena potkanovi. Úspěšná implementace této metody na 9,4 T MRI systému znamená, že může být použita také na MR zobrazovacích systémech s nižšími magnetickými poli.
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Segmentation of cardiac tissue fibrosis in MRI data
Sokol, Norbert ; Mézl, Martin (referee) ; Kolář, Radim (advisor)
Late gadolinium enhancement cardiovascular magnetic resonance imaging can be used to visualize pre-ablation fibrosis or post-ablation myocardial scar. This can significantly helps patients with myocardial fibrosis to determine region of fibrosis and for post-operative validation of intervention after radio-frequency catheter ablation. In this thesis, i introduce an algorithm for successful distinguish of fibrosis on datasets of patients with myocardial fibrosis, scanned at Faculty hospital at St. Anne’s University Hospital.
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