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Multi-tensor model based tractography of axonal bundles
Piskořová, Zuzana ; Jiřík, Radovan (referee) ; Labounek, René (advisor)
Cílem semestrální práce je návrh trasovacího algoritmu, který zohledňuje mikrostrukturní vlastnosti nervové tkáně. K této problematice je sepsána rešerše obsahující úvod do problematiky. Je zde popsán jev difuze, princip difuzně váženého MRI a odhad profilu anizotropní difuze. K podrobnější analýze byl vybrán algoritmus COMMIT, u kterého byla navržena alternativní optimalizační metoda.
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Segmentation in the color fundus imges
Malínský, Miloš ; Jiřík, Radovan (referee) ; Kolář, Radim (advisor)
Optic nerve head and macula are important structures in fundus images. Detection and measurement plays crucial role in several diagnosis methods of optic disease. This work is focused on the detection of the central point of macula and optic nerve head, where the inner border is detected too. There are many methods for extracting this structure in retinal images. Due to the unique properties of each acquisition technique, a single generally acknowledged detection algorithm does not exist. The whole detection process is described from preprocessing through segmentation towards postprocessing. Presented methods are based on the combination of correlation techniques, Hough transform, active contours and morphological operations. The detected contours of the optic nerve head are evaluated and quantitatively compared with the contour drawn by experienced ophthalmologist. The master thesis contains quantity of images that help to describe detection methods.
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Quality assessment of retinal images
Tvarůžek, Marek ; Jiřík, Radovan (referee) ; Kolář, Radim (advisor)
This thesis deals with the properties of retinal images, which are taken with a digital fundus camera. The basic image processing operations are described and applied on biomedical images. Based on these operations, the algorithm for image quality assessment is designed and implemented in Matlab. The quality metrics quantify the focusing. The proposed methods are tested on two datasets and the results are presented and discussed.
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Segmentation in microscopic images
T.Kovács, Matúš ; Jiřík, Radovan (referee) ; Kolář, Radim (advisor)
This thesis deals with the segmentation of microscopic images from plant sections. It describes the importance of the histogram for obtaining information from the image, and the utilization of the wavelet transformation for the preprocessing of the images. The thesis describes and categorizes different segmentation methods. In the thesis we use MATLAB for the validation of the presented theories and as the interface for creating a software model. The created software application automatically analyzes and evaluates microscopic images.
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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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Measurement of Dialyser-Membrane Diffusion Coefficient
Kašák, Pavel ; Bartoš, Michal (referee) ; Jiřík, Radovan (advisor)
This thesis focuses on the measurement of diffusion coefficient of dialysis membrane. The first part describes possibilities of membrane modelling. Basic models, which allow us to determine the basic characteristics of dialysis membranes like permeability and diffusion coefficient, are described. Next chapter deals with basic types and properties of membranes. The main part focuses on making the experimental installation, which is used to simulate permeance of contrast agent, used in DCE-MRI, through dialysis membrane. The last theoretical chapter describes calculations used to estimate diffusion coefficient. Practical part of this thesis uses a designed experimental installation for estimation of diffusion coefficient for two contrast agents Gadovist® and Multihance®.
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Automatic detection of neural fibers losses
Václavek, Martin ; Jiřík, Radovan (referee) ; Kolář, Radim (advisor)
This work is focused on detection of loss in nerve fibre layer on colour pictures of retina, witch are makes by fundus camera. It describe every simple objects of retina, optic nerve head, macula lutea and vascular bed. It detect optic nerve head and his near area, witch is general for detection of breakdownds. It use several metodes of picture adjusting for picture elaboration and objects detection (segmentation, thresholding, enhancement, hough transformation ). The detection of loss in nerve fibre layer is based on comparing of statistic parameters ( average, standart deviation, skewness coefficient and kurtosis coefficient histogram, entropy ) in choosed areas with and withou destruction of nerve layers. Vascular bed have badwatsh on results, cause of this we using hand choosing of essay.
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Image registration
Jindra, Jakub ; Jiřík, Radovan (referee) ; Krátká, Lucie (advisor)
This bachelor thesis deals with various methods of image registration in the medical treatment. The criterias are elaborated for selecting the correct method of registration. This work describes parameters for proper transformation, identification, registration proces, a final assessment of registration for its approval and the corresponding evaluation. Some basic programs have already concerned with image registration and they are accompanied by basic information. This semester thesis also describes the basics of working with MRI and the creation of anatomical atlas from the magnetic resonation rat’s brain. In conclusion is described the creation of a simple graphical interface for viewing images of brain obtained from the magnetic resonance. Furthermore, the work deals with the registration of images according freely available programs and the related system of evaluation of these results. The scoring system is processed in a graphical users interface Matlab, where is used histograms, mosaic and evaluation using the cross.
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Using multi-echo sequences in DSC-MRI
Černý, Štěpán ; Jiřík, Radovan (referee) ; Macíček, Ondřej (advisor)
The task of this thesis is to study the subject of perfusion analysis based on dynamic imaging with T2/T2* contrast. The focus was on the acquisition commonly used for DSC-MRI and especially in the acquisition pulse sequences that use images with different echo time, so called Multi-echo sequence. Principles of dynamic measurement by magnetic resonance imaging, the role of contrast agents and their influence on the relaxation times are described. It also describes the problems perfusion analysis, measurement and mathematical modeling parameters entering to the convolution dependency for getting perfusion parametersIn the experimental part is developed automatic algorithm to gain curves relaxation time T2 *. Next, the synthetic data are created and tested robustness estimate perfusion parameters against noise. In the next phase of work there are compared real scanned objects with using a conversion with T2 * and free of T2*. In the last phase of work is compared influence of length of used echo times on concentration curves and after perfusion analysis influence on resulting perfusion parameters.
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Segmentation of the basic parts of human brain in MR data
Klásek, Pavel ; Jiřík, Radovan (referee) ; Malínský, Miloš (advisor)
This work describes segmentation methods used in image data processing, from which there are selected and implemented suitable methods for solving the assignment of segmentation parts of human brain – region growing and watershed algorithm. Segmentation techniques are realized on real data sources. Final segmentation results are presented, compared and evaluated accordig to the advanced software FreeSurfer segmentation results. In addition there is a list of available software that can be applied for the purpose of neurological image segmentation.
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