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Image Registration - Application in ophthalmology and ultrasonography
Harabiš, Vratislav ; Matula,, Petr (referee) ; Zemčík, Pavel (referee) ; Kolář, Radim (advisor)
Image registration is widely used in clinical practice. However image registration and its~evaluation is still challenging especially with regards to new possibilities of various modalities. One of these areas is contrast-enhanced ultrasound imaging. The time-dependent image contrast, low signal-to-noise ratio and specific speckle pattern make preprocessing and image registration difficult. In this thesis a method for registration of images in ultrasound contrast-enhanced sequences is proposed. The method is based on automatic fragmentation into image subsequences in which the images with similar characteristics are registered. The new evaluation method based on comparison of perfusion model is proposed. Registration and evaluation method was tested on a flow phantom and real patient data and compared with a standard methods proposed i literature. The second part of this thesis contains examples of application of image registration in~ophthalmology and proposition for its improvement. In this area the image registration methods are widely used, especially landmark based image registration method. In this thesis methods for landmark detection and its correspondence estimation are proposed.
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Simulation of ultrasound sequences in contrast mode
Staňková, Jana ; Hesko, Branislav (referee) ; Harabiš, Vratislav (advisor)
This bachelor thesis deals with the principle of contrast imaging techniques for ultra-sound imaging. In the first part there are described basic principles and characteristics of ul-trasound 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 mo-dels with a focus obtain perfusion parametres and analyze perfusion curves obtained by mea-suring the ultrasound contrast agent over time. The second part is devoted to designing a pro-gram for generating simulated ultrasound images and description of the simulation of 2D ul-trasound tomograms.
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Modelling in perfusion MR imaging
Válková, Hana ; Jiřík, Radovan (referee) ; Kratochvíla, Jiří (advisor)
This thesis deals with the magnetic resonance perfusion data analysis especially DCEMRI. In its introduction the thesis describes the problem of DCE-MRI data aquisition, the necessity of appropriate contrast agent and basic principles of perfusion analysis. The dynamic behavior of contrast agent vascular distribution can be described by arterial input function (AIF). The shape of the curves close to the area of interest is affected by dispersion which is called vascular transport function (VTF) due to the distribution of the contrast agent to the region of interest. Finally the tissue residual function describes system behavior of tissue. The practical part of the diploma thesis is aimed at implementation of model curves AIF, VTF and TRF. Furthermore, a simulation program was created for easy manipulation with introduced models moreover the program is used to perform an estimation of perfusion parameters based on nonblind deconvolution. The method is validated on synthetic data and illustrated on clinical data of the renal cell carcinoma patient.
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Perfusion Modelling in Optical Coherence Tomography
Štohanzlová, Petra ; Penhaker,, Marek (referee) ; Kudrna,, Petr (referee) ; Kolář, Radim (advisor)
This thesis deals mainly with perfusion modeling in optical coherence tomography (OCT). The introductory part deals with basic theory of the OCT, including a description of its basic applications. Part of the work was the testing of selected contrasting materials suitable for the OCT and the design and implementation of phantoms, which were subsequently used in the main part of the thesis. In the practical part, attention is paid to the perfusion analysis in the OCT, first the application of the dilution theory in the OCT for flow estimation, then a study testing the basic theory of perfusion on OCT by means of tissue phantom. Another part of the thesis is devoted to the method of speckle variance analysis for flow visualization.
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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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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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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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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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