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Internet library of methods and algorithms used for medical image registration
Koňařík, Jakub ; Jiřík, Radovan (referee) ; Peter, Roman (advisor)
Image registration is a procedure which is heading to search for a geometric transformation, which ensures same position, orientation and size of coresponding objects in pictures. How does these methods work? These methods and principies are explained in first part of this work. Second part of this work is aimed to explain theory about information systems and practical creation of the internet databaze. These practical part was realized in editorial system called Drupal.
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Evaluation of dental pulp treatment based on the X-ray micro computed tomography
Břínek, Adam ; Jiřík, Radovan (referee) ; Zikmund, Tomáš (advisor)
This work deals with processing and analysis of micro-CT images of dental-canals filled by~two materials (AH-plus and NaMPC). For that reason, six dog-teeth were scanned in the X-Ray Micro CT Research Lab. The main aim was to produce an algorithm (in Matlab) that evaluates the quality of filling of dental canals (quality of filling materials). The algorithm performs the segmentation of dental canals and calculates their borders. Also, the algorithm measures the percentage contacts of filling materials with dental walls. Moreover, the algorithm provides masks of dental canals according to requirements of the commercial program VG Studio, that evaluates the porosity of filling materials. The results of percentage contacts and porosities show on not-remarkable differences of tested filling materials.
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Application of mathematical methods for object detection in ultrasound B-image
Ruttner, Michal ; Jiřík, Radovan (referee) ; Sedlář, Martin (advisor)
This work deals with the detection of objects in ultrasound B-image. First we will become familiar with the ultrasound device and its functions.We will demonstrate various kinds of imaging techniques used in ultrasound diagnostic imaging. Further we will be concerned with medical image processing. We will describe the functions of some edge detectors based on the first derivation, detectors based on the second derivation, detectors based on approximation of parametric model and detectors of borders or lines. Otherwise we will find out how to do preprocessing, Some of these methods we will try on different images for sharpening of image and enhacment of contoure. Using the program created in MATLAB©, we will use process imaging on internal carotid images. In conclusion we will evaluate the results.
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Multichannel Image Deconvolution
Bradáč, Pavel ; Kolář, Radim (referee) ; Jiřík, Radovan (advisor)
This Master Thesis deals with image restoration using deconvolution. The terms introducing into deconvolution theory like two-dimensional signal, distortion model, noise and convolution are explained in the first part of thesis. The second part deals with deconvolution methods via utilization of the Bayes approach which is based on the probability principle. The third part is focused on the Alternating Minimization Algorithm for Multichannel Blind Deconvolution. At the end this algorithm is written in Matlab with utilization of the NAG C Library. Then comparison of different optimization methods follows (simplex, steepest descent, quasi-Newton), regularization forms (Tichonov, Total Variation) and other parameters used by this deconvolution algorithm.
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Acquisition contrast of X-ray projection and projection-reconstruction imaging
Zubal, Lukáš ; Jiřík, Radovan (referee) ; Drastich, Aleš (advisor)
The work resulted in computer application which simulates X-ray projection and projection-reconstruction imaging in voxel space. Application user becomes acquainted with terms of acquisition contrast of X-ray projection and projection-reconstruction imaging. The thesis takes detailed look at algorithms of computing ray integrals and X-ray projection and projection-reconstruction imaging. The potential of modern computer graphics is also discussed.
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Measurements of permeability of dialysis membranes
Veselá, Martina ; Jiřík, Radovan (referee) ; Kolářová, Jana (advisor)
Familiarization with dialysis theoretical principles and determination of dialysis membrane permeability with the help of experimentally assembled apparatus is the aim of this bachelor thesis. The introduction part deals with basic knowledge concerning treatment with dialysis and its current quality. There continues a chapter stating an overview of dialysis membranes different types and main characteristics of individual materials, which the membranes were made of and which they are produced now. Theoretical preparation for the practical part of the thesis clarifies the basic notions, principals and processes connected with the mass transfer through dialysis membranes and dialysis. Further on, theoretical process is described and phrased how to determine dialysis membranes permeability in a laboratory scale in an experimental way. Two possible configurations of experimental apparatus are illustrated with block schemes working either in a non-stationary or a stationary regime of measurement. The basis to determine membrane permeability is sampling in specified time intervals from blood and dialyze side and spectrophotometric detection of samples concentration. The practical part itself is preceded with the process with collected samples analysis. Then, it is followed with relations derivation for mass transfer coefficient calculation. Concentration progress on blood and dialyze side with non-stationary way of measurement is modelled in Simulink programme. The practical part of the thesis uses the mentioned above theoretical knowledge and assumptions and it realises concrete measurements in non-stationary regime. Evaluating part of the thesis documents the obtained results and assesses them with the help of derived equations. The whole process of measurement including obtained results is evaluated and discussed in the final part.
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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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Modelling for ultrasound perfusion imaging
Jakubík, Juraj ; Jiřík, Radovan (referee) ; Mézl, Martin (advisor)
This master thesis deals with the contrast agents and their application in the ultrasound perfusion analysis. It is focused on Bolus & Burst method which, as a combination of two approaches that have been used so far, allows an absolute quantification of perfusion parameters in the region of interest. Contrast agent concentration time sequence is modeled as a convolution of the parametrically defined arterial input function and the tissue residual funkction. Thesis discusses different mathematical models of these functions as well as the methods of the parameters estimation. The methods functionality is validated on simulated and also preclinical data.
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Quantification of Relaxation Time T1 in DCE-MRI
Vitouš, Jiří ; Mézl, Martin (referee) ; Jiřík, Radovan (advisor)
This bachelor thesis deals with methods of T1 relaxation time quantification and B1 magnetic field inhomogeneities corrections. For purposes of the required measurements, the phantom was created using a 3D printer. Firstly the thesis presents information about a given theme, then it hands out the results of measurements taken using standard quantification methods. These methods are consequently analyzed and compared. Next part of the bachelor thesis deals with the fast method based on a variable flip angle (VFA), which needs a magnetic field B1 correction maps to give reasonable T1 estimates. For this purpose, two methods of B1 correction are presented. The first method is a double angle method and second is based on mapping magnetic field B1 using a reference T1 map. To decide which T1 map of which method should be used as a reference, a simple simulation is proposed, which describes the impact of unfavorable effects, such as B1 itself, on the T1 estimate of standard methods. In the end, the conclusions are made and the results of VFA methods are compared with standard methods of quantification.
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