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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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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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Acquisition, Modeling and Signal Processing in Ultrasound Perfusion Imaging
Mézl, Martin ; Kozubek, Michal (referee) ; Flusser,, Jan (referee) ; Jiřík, Radovan (advisor)
This work deals with possibilities of ultrasound perfusion analysis for the absolute quantification of perfusion parameters. In the theoretical part of this work are discussed possibilities of using of the ultrasound contrast agents and approaches for the perfusion analysis. New methods for the perfusion analysis are suggested and tested in the practical part of this work. The methods are based on convolutional model in which the concentration of the contrast agent is modeled as aconvolution of the arterial input function and the tissue residual function. The feasibility of these methods for the absolute quantification of perfusion parameters is shown on data from phantom studies, simulations and also preclinical and clinical studies. The software for the whole process of the perfusion analysis was developed for using in hospitals.
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Batch processing of perfusometric MRI data
Filipová, Petra ; Macíček, Ondřej (referee) ; Jiřík, Radovan (advisor)
This diploma thesis deals with the DCE – MRI method (Dynamic contrast enhanced magnetic resonance imaging). Basic principle of magnetic resonance and pulse sequence is described. The diploma thesis focuses on the DCE method, especially on the description of the processing procedure by this method. Description of selected pharmacokinetic models is the part of this diploma thesis as well. Furthermore, description and realization of batch processing by PerfLab system is presented. For verifying purposes of the batch processing functionality real data were measured using created acquisition protocol, which is also part of the diploma thesis.
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Perfusion analysis using DSC-MRI method
Minsterová, Alžběta ; Jiřík, Radovan (referee) ; Macíček, Ondřej (advisor)
This bachelor thesis deals with the DSC (Dynamic Susceptibility Contrast) method, which is one of the magnetic resonance imaging methods using a contrast agent. It describes the principle of the magnetic resonance imaging, other methods of MRI using the contrast agent are mentioned. It further contains the DSC-MRI method, common used sequences and the description of a procedure of an imaging by this method. This thesis also focuses on the implementation of a graphical application in MATLAB, which copes with the perfusion analysis and the visualization of perfusion maps.
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Modelling for ultrasound perfusion imaging
Hracho, Michal ; Šikner, Tomáš (referee) ; Mézl, Martin (advisor)
This thesis deals with the possibilities of determining perfusion parameters of vascular system, using contrast-enhanced ultrasound imaging, which is non-invasive method. Properties of ultrasonography and use of contrast agents are briefly summarized. The methods selected for perfusions analysis were Bolus-tracking¬¬, Burst-replenishment and both of them combined – Bolus&Burst. Parametric models based on these methods were created for modelling an approximation of set perfusion parameters with the use of blind deconvolution.
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Advanced Methods of Perfusion Analysis in MRI
Macíček, Ondřej ; Frollo, Ivan (referee) ; Mikl, Michal (referee) ; Jiřík, Radovan (advisor)
This dissertation deals with quantitative perfusion analysis of MRI contrast-enhanced image time sequences. It focuses on two so far separately used methods -- Dynamic contrast-enhanced MRI (DCE-MRI) and Dynamic susceptibility contrast MRI (DSC-MRI). The common problem of such perfusion analyses is the unreliability of perfusion parameters estimation. This penalizes usage of these unique techniques on a regular basis. The presented methods are intended to improve these drawbacks, especially the problems with quantification in DSC in case of contrast agent extravasation and instability of the deconvolution process in DCE using advanced pharmacokinetic models. There are a few approaches in literature combining DCE and DSC to estimate new parameters of the examined tissue, namely the relaxivity of the vascular and of the interstitial space. Originally, in this scheme, the 2CXM DCE model was used. Here various models for DCE analysis are tested keeping in mind the DCE-DSC combination. The ATH model was found to perform better in this setting compared to 2CXM. Finally, the ATH model was used in alternating DCE-DSC optimization algorithm and then in a truly fully simultaneous DCE-DSC. The processing was tested using simulated and in-vivo data. According to the results, the proposed simultaneous algorithm performs better in comparison with sequential DCE-DSC, unleashing full potential of perfusion analysis using MRI.
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Evolution algorithms for ultrasound perfusion analysis
Kolářová, Jana ; Odstrčilík, Jan (referee) ; Mézl, Martin (advisor)
This master´s thesis is focused on the application of evolutionary algorithms for interleaving data obtained by ultrasound scanning of tissue. The interleaved curve serves to estimate perfusion parameters, thus allowing to detect possible pathophysiology in the scanned area. The theoretical introduction is devoted to perfusion and its parameters, contrast agents for ultrasonic application, ultrasonic modality scanning, optimization, evolutionary algorithms in general and two selected evolutionary algorithms - genetic algorithm and bee algorithm. These algorithms were tested on noisy data obtained from clinical images of mice with tumor. The final part summarizes the results of the practical part and provides suggestions and recommendations for further possible development.
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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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Simulation of ultrasound sequences in contrast mode
Staňková, Jana ; Mézl, Martin (referee) ; Harabiš, Vratislav (advisor)
This bachelor thesis deals with the principle of contrast imaging techniques for ultrasound imaging. In the first part there are described basic principles and characteristics of ultrasound waves for the understanding. It is also focused on ultrasound contrast agents used in contrast enhanced ultrasound imaging. The important part is the description of perfusion models with a focus on obtaining perfusion parametres and analyzing perfusion curves obtained by measuring the ultrasound contrast agent over time. The second part is devoted to designing a program for generating simulated ultrasound images and description of the simulation of 2D ultrasound tomograms.
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