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Modeling and Signal Processing in Dynamic Contrast Enhanced Magnetic Resonance Imaging
Kratochvíla, Jiří ; Šroubek,, Filip (referee) ; Tintěra,, Jaroslav (referee) ; Jiřík, Radovan (advisor)
The theoretical part of this work describes perfusion analysis of dynamic contrast enhanced magnetic resonance imaging from data acquisition to estimation of perfusion parameters. The main application fields are oncology, cardiology and neurology. The thesis is focused on quantitative perfusion analysis, specifically it contributes to solving of the the main challenge of this method – correct estimation of the contrast-agent concentration sequence in the arterial input of the region of interest (arterial input function). The goals of the thesis are stated based on literature review and on the expertise of our group. Blind deconvolution is selected as the method of choice. In the practical part of this thesis, a new method for arterial input function identification based on blind deconvolution is proposed. The method is designed for both preclinical and clinical applications. It was validated on synthetic, preclinical and clinical data. Furthermore, possibilities of the longer temporal sampling provided by blind deconvolution were analyzed. This can be used for improved spatial resolution and possibly for higher SNR. For easier deployment of the proposed methods into clinical and preclinical use, a software tool for perfusion data processing was designed.
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Measurement and processing of diffusion data from magnetic resonance
Vankó, Bence ; Jiřík, Radovan (referee) ; Kolářová, Jana (advisor)
This bachelor thesis deals with DTI examination. The diffusion tensor model of magnetic resonance imaging is a modern diagnostic method mainly used to visualize the spatial relationship of a particular neuronal pathway of the brain. The work is divided into three main parts. The first part contains the theoretical introduction to MRI, DTI and literary research from individual scientific articles dealing with DTI experiments. The second part of the thesis deals with the search of electronic articles to choose the right acquisition. Based on the articles being studied, parameters were selected and polished during the measuring of the phantom. In the third part, the measurements are done on the basis of the resulting acquisition protocol and the data is processed in various software.
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Fingerprint biometry
Kubica, Roman ; Jiřík, Radovan (referee) ; Fedra, Petr (advisor)
The first part of this thesis deals with principles of evaluation biometric methods of scanning fingerprint images. Classification and description of single methods, separated into groups depending on the algorithm of comparison of template and image from database are included. In the next part is thesis focused on evaluation based on the success of experimental results and description of available databases. The main purpose of this thesis is creation of computer program for identification of fingerprint image in the programming interface MATLAB®. Realized identification algorithm is based on computing of Poincare index and extraction of singular points and minutiae. Performance of the program is tested on generated database and evaluated by index FAR and FRR.
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Arterial Spin Labeling MRI Data Analyzation
Galanová, Zuzana ; Jiřík, Radovan (referee) ; Krátká, Lucie (advisor)
This bachelor´s thesis is focusing mostly on perfusion imagining, which is done by the method of arterial spin labeling. It describes physical basics of nuclear magnetic resonance, image reconstruction, perfusion imagining without contrast substances, principles of arterial spin labeling and different ways of arterial spin labeling – mostly FAIR-RARE sequence, which belongs to the pulsed arterial spin labeling. One part of the thesis is dedicated to production of perfusion map in Matlab. Results are evaluated by comparison of data produced in Matlab and data produced in Paravision Version 5.1 and they are discussed.
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Automatic Processing of DCE-MRI Data
Karela, Jiří ; Mézl, Martin (referee) ; Jiřík, Radovan (advisor)
This master thesis deals with the issue of automatic processing of DCE-MRI data. It describes some important procedures and methods. The work is divided into theoretical part, practical part and conclusion. The theoretical part mainly describes some methods, on the basis of which the practical part was then solved. However, another theory related to the topic is also described here. The practical part then builds on the theory and solves the problem of automatic detection of arterial voxels and the concentration of contrast agent in the arteries. The algorithms are tested on rat brain data obtained from DCE-MRI. The conclusion serves as a summary and evaluation of our results. It also serves as a reflection on the implementation of our methods.
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Comparison of Pharmacokinetic models for DCE-MRI
Bačovská, Kristýna ; Mézl, Martin (referee) ; Jiřík, Radovan (advisor)
This thesis deals with perfusion analysis using DCE-MRI (Dynamic contrast-enhanced magnetic resonance imaging). DCE-MRI is commonly used for microcirculation evaluation mainly in oncology and in recent years also in cardiology. The theoretical overview focuses on the issue of pharmacokinetic modeling and the estimation of perfusion parameters using selected models. The experimental part describes research software PerfLab and then it is aimed at the proposed program for synthetic data generation. Simulated data obtained under ideal conditions and in the presence of noise were used to compare models for the accuracy and reliability of DCE-MRI analysis.
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Registration of Ultrasound Image sequences
Kubica, Roman ; Mézl, Martin (referee) ; Jiřík, Radovan (advisor)
The result of this thesis, focused on medical image registration, is an automatic image registration algorithm. It is constructed to be used on real ultrasonography images, created by perfusion imaging. In its introductory part, the thesis deals with registrations methods, next it describes types of optimization principles and single criteria functions served to determine correct image transformation. Based on the theoretical part, there are realized three optimization algorithms using three criterial functions, which served to registration of provided ultrasonography sequences. These algorithms are tested and results are passed on analysis, on its ground are judged its advantages and disadvantages.
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Comparison and assessment of single-echo and multi-echo BOLD fMRI acquisition
Kovářová, Anežka ; Jiřík, Radovan (referee) ; Mikl, Michal (advisor)
This master’s thesis deals with functional magnetic resonance and monitoring of the effect of acquisition acceleration methods on the quality of functional images and observed BOLD signal. The basic principles of magnetic resonance imaging, the explanation of the specifics of functional magnetic resonance and the formation and scanning of BOLD signal are described here. Subsequently, there is the definition of fMRI experiment and description of sequences used for fMRI, focusing on aquisition acceleration techniques. The influence of sequence parameters on image quality and the data processing methods are explained aftewards. The practical part describes the parameters of used sequences, the acquisition procedure and the task for the subject during aquisition. Data from 26 healthy volunteers were obtained and analyzed afterwards. Based on this, the differencesbetween the different sequence variants were evaluated and the initial assumption that the multi-echo acquisition yields better results with faster measurements than single-echo was confirmed.
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Measurement of ultrasound speed
Pouč, Petr ; Roleček, Jiří (referee) ; Jiřík, Radovan (advisor)
The thesis deals with the ultrasonic velocity measurement. The ultrasonic velocity was determined on basis of ultrasonic flight time from a transmitter to a receiver. Three methods how to determine the ultrasonic velocity in medium were proposed. Special algorithms have been created and later on build in the developed program. All the software was developed in Agilent VEE Pro 8.5. The thesis contains a proposal of two experiments tutorials for the department of Biomedical engineering that will be used during experimental lessons. The experiments deal with ultrasonic velocity measurement.
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Image processing of MRI
Němcová, Simona ; Jiřík, Radovan (referee) ; Krátká, Lucie (advisor)
This thesis deals with the cartilage imaging using magnetic resonance. At first, there is mentioned physical principle of the magnetic resonance phenomenon and the most commonly used excitation sequences, followed by the description of the 9.4 T MR imaging system Bruker BioSpec 94/30 USR, which was used for measurement in the practical part. The next part is dedicated to the composition of cartilages and describes the temporomandibular joint, due to its suitability as an object for cartilage imaging. The series of MR scans of temporomandibular joint were taken with different acquisition parameters and evaluated by program designed through the MATLAB software. The program can be used for viewing scanned images, evaluating their contrast and determining the T1 relaxation time of the tissues by creating T1 maps.
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