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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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Data analysis for quantitative MR relaxometry
Páralová, Hana ; Jiřík, Radovan (referee) ; Mézl, Martin (advisor)
Tato práce se zabývá implementací algoritmu pro analýzu dat pro kvantitativní relaxometrii magnetické rezonance. Magnetická rezonance (MR) je neinvazivní zobrazovací technika využívající magnetických vlastností atomových jader. Motivací pro využívání relaxačních parametrů tkání je nezávislost na MR skenerech či jednotlivých pacientech. V práci jsou popsány nezbytné teoretické základy MR mechanizmů a vzniku kontrastu v obrazech. S jejich využitím je navržen algoritmus v jazyce Python pro fitování relaxačních parametrů vzorku. Fitování probíhá podle exponencíálních modelových funkcí pro tři různé kombinace parametrů - individuální fitování T1 nebo T2 relaxačního času a simultánní fitování obou časů. Pro výpočet směrodatné odchylky fitovaných parametrů je použit lokálně linearizovaný model a dolní meze podle teorie Cramér-Rao. Výsledky práce byly úspěšně ověřeny na relaxometrii fixovaného potkaního mozku.
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Parallelization of complex tasks in reconstruction of dynamic magnetic resonance
Bijotová, Kateřina ; Rajmic, Pavel (referee) ; Mašek, Jan (advisor)
This thesis deals with parallelization of complex tasks in reconstruction of dynamic magnetic resonance. It describes the basic principle of magnetic resonance and its relation to Fourier transform. It deals with the difference between static and dynamic magnetic resonance image reconstruction. It analyzes SVD algorithm and its use in magnetic resonance image reconstruction. It presents the principles and the importance of parallel computing in magnetic resonance imaging and describes CUDA technology. The thesis also contains a description and execution of the implementation of the reconstruction model in MATLAB and Java programming language which were optimized by JCuda library for Java implementation and gpuArray function in case of MATLAB implementation.
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Parallelization of complex tasks in reconstruction of dynamic magnetic resonance
Bijotová, Kateřina ; Rajmic, Pavel (referee) ; Mašek, Jan (advisor)
This thesis deals with parallelization of complex tasks in reconstruction of dynamic magnetic resonance. It describes the basic principle of magnetic resonance and its relation to Fourier transform. It deals with the difference between static and dynamic magnetic resonance image reconstruction. It analyzes SVD algorithm and its use in magnetic resonance image reconstruction. It presents the principles and the importance of parallel computing in magnetic resonance imaging and describes CUDA technology. The thesis also contains a description and execution of the implementation of the reconstruction model in MATLAB and Java programming language which were optimized by JCuda library for Java implementation and gpuArray function in case of MATLAB implementation.
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Compatibility of selected dental alloys with magnetic resonance imaging
Linetskiy, Igor ; Hubálková, Hana (advisor) ; Suchánek, Jakub (referee) ; Dostálová, Taťjana (referee)
Magnetic resonance imaging (MRI) is one of the up-to-date and perspective methods of diagnostic medical imaging. It is highly valued for absence of ionizing radiation, non-invasiveness, acquiring of highly accurate images of hard and especially soft tissues in any plane. It is a method of choice in central nervous system imaging. Nowadays it is used in diagnostics of other diseases in the maxillofacial area. The major shortcoming of MRI is interaction of magnetic fields of MRI system with metallic objects present in human body. As a result, this may lead to their heating, movement, and also to imaging artifacts. Since different metallic constructions (fixed bridges, dental implants, splints, plates, orthodontic appliances, etc.) are often used in the contemporary dentistry, the problem of their compatibility with MRI is relevant. The aim of this study was to validate the compatibility of dental alloys with MRI, classify the materials according to the degree of compatibility and to establish the range of their possible negative impact on quality of MRI in head and neck area. In order to find dental metals and alloys, General Health Insurance Company code- list, catalogues of manufacturers' and Prague dental labs were used. Measurement methods of magnetic susceptibility (MS), electric conductivity...
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T cells labelling by bimodal contrast agent for in vivo studies of stroke
Krijt, Matyáš ; Poljaková, Jitka (advisor) ; Kříž, Jan (referee)
Stroke is a serious brain injury, which causes sudden death or terminates in permanent neurological disability. Nowadays, tissue plasminogen activator (tPA) is used as the only effective treatment of stroke. One of the potential targets for novel therapy are T cells. Even though the explicit role of T cells in the pathogenesis of brain injury, amounts and timing of all T cell subtypes infiltrating into brain during the stroke still needs further investigation. The research in this field is complicated by the lack of efficient methods for in vivo cell tracking. Therefore the aim of this thesis was to develop a method of T cells labelling by MRI contrast agent in order to investigate T cells distribution in ischemic mice model using in vivo MR imaging. T cells were isolated from C57/BL6 mice in two step isolation protocol using gradient centrifugation and magnetic separation with the efficiency of 97 %. The isolated cells were labelled with 100 μg Fe/mL of Molday ION Rhodamine B contrast agent. The labelling efficiency after 17 hours of cells incubation was higher than 99 %. The labelled cells were cultured with CD3 and CD28 antibodies resulting into the 74 % viability of labelled T cells compared to 83 % viability of non labelled T cells. The labelled T cells were visualized by fluorescent...
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Multiple sclerosis - clinical and paraclinical markers for monitoring disease activity and factors influencing its course
Šťastná, Dominika ; Horáková, Dana (advisor) ; Libertínová, Jana (referee) ; Taláb, Radomír (referee)
Multiple sclerosis (MS) is a chronic neurological disease that, without treatment, leads over years to decades to severe disability in most patients. We cannot cure the disease, but there is growing evidence that early initiation of anti-inflammatory therapy and management of associated comorbidities has a major impact on its course. Patient registries have an irreplaceable contribution to evaluating factors influencing the MS course and the monitoring of therapeutic agents in real clinical practice. First, this thesis evaluated therapy management trends between 2013 and 2021 based on data from the Czech National MS Registry (ReMuS). Subsequently, the paper responds to the onset of the covid-19 pandemic through registry data and addresses this issue in the context of MS. The proportion of patients in ReMuS treated with high-efficacy disease-modifying therapies (HE-DMT) increased from 16.2% to 37.1% between 2013 and 2021, and the proportion of treatment-naive patients initiating HE-DMT increased from 2.1% to 18.5%. Regarding covid-19 infection, we determined that higher body mass index, older age, recent high-dose glucocorticoid treatment, and anti-CD20 therapy were independent variables associated with pneumonia based on data from 958 MS patients with a history of covid-19. Further, we analyzed...
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Coregistration of diffusion weighted MRI data with high b-values
Špaček, Vojtěch ; Říha, Pavel (referee) ; Vojtíšek, Lubomír (advisor)
This bachelor thesis deals with the coregistration of diffusion-weighted MRI data with high b-values. The aim is to compare selected coregistration methods on real data and to quantify the quality of the output. The theoretical part presents the principle of diffusion imaging, the effect of b-value on the image and different methods of data preprocessing with a focus on the possibilities of coregistration of images with varying contrast. In addition, available software tools and methods for assessing the quality of coregistration are introduced. In the practical portion of the paper, preprocessing of diffusion data, including coregistration by the selected methods, is performed and the quality is analyzed using statistical measures.
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