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Software for patients and brain regions selection suitable for analysis of connectivity in fMRI
Slavíček, Tomáš ; Lamoš, Martin (referee) ; Jan, Jiří (advisor)
The aim of this thesis is to create an exploratory tool for functional magnetic resonance imaging data, which allows quickly and easily making a selection of persons and areas suitable for group analysis of connectivity. In the first chapters of this work is mentioned history of brain research and comparison of methods used in functional imaging. Next they are discussed the theoretical basis of fMRI methods, such as the formation of BOLD signal, acquisition parameters of MRI images and methods for designing experiments. The following chapter describes in detail the analysis of recorded data from the pre-processing to the interpretation of results. The last chapter of the first part describes problems of group analysis in SPM8 software. The second half of this work is dedicated to the description of developed program from data input to saving the results, including detailed descriptions of key features. In conclusion, there is a chapter characterizing the application of developed program on real data from clinical studies, including the results and evaluation of the usability of program. The program will mainly be used in neuroscience research.
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Digital radiography- image processing simulation
Lamoš, Martin ; Kolář, Radim (referee) ; Drastich, Aleš (advisor)
This paper describes a MATLAB application with the main purpose of the simulation of noise components and noise elimination methods of Digital Radiography. The main parts of simulator are the model of a scene, procedures for loading the noise components to image data and methods for image processing. Various methods are employed depending on the type of noise. Subtraction techniques are used for the elimination of structural noise. The physical noise suppression is obtained using several methods of cumulation and Pixel Shift is used to reduce motion artifacts caused by the existence of moving noise. The techniques of superposition highlight the areas of interest in an image. Included are also auxiliary procedures for simulator running and presentation of final data. The model and the presented application can be used mainly for educational purposes as a powerful didactic tool.
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Service Messenger for Windows
Popelka, Petr ; Lamoš, Martin (referee) ; Sekora, Jiří (advisor)
This thesis describes the process of communication in Ethernet based on TCP/IP model. Client – server application was designed and realized using this model. This application can be used to send service messages between groups of doctors and workplace of OKB in FN Brno. This thesis also describes current laboratory equipment and communication between them laboratory information system using the protocol ASTM. This communication can be later used to develop other features of the designed application.
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Influence of parcellation atlas on quality of classification in patients with neurodegenerative dissease
Montilla, Michaela ; Lamoš, Martin (referee) ; Gajdoš, Martin (advisor)
The aim of the thesis is to define the dependency of the classification of patients affected by neurodegenerative diseases on the choice of the parcellation atlas. Part of this thesis is the application of the functional connectivity analysis and the calculation of graph metrics according to the method published by Olaf Sporns and Mikail Rubinov [1] on fMRI data measured at CEITEC MU. The application is preceded by the theoretical research of parcellation atlases for brain segmentation from fMRI frames and the research of mathematical methods for classification as well as classifiers of neurodegenerative diseases. The first chapters of the thesis brings a theoretical basis of knowledge from the field of magnetic and functional magnetic resonance imaging. The physical principles of the method, the conditions and the course of acquisition of image data are defined. The third chapter summarizes the graph metrics used in the diploma thesis for analyzing and classifying graphs. The paper presents a brief overview of the brain segmentation methods, with the focuse on the atlas-based segmentation. After a theoretical research of functional connectivity methods and mathematical classification methods, the findings were used for segmentation, calculation of graph metrics and for classification of fMRI images obtained from 96 subjects into the one of two classes using Binary classifications by support vector machines and linear discriminatory analysis. The data classified in this study was measured on patiens with Parkinson’s disease (PD), Alzheimer’s disease (AD), Mild cognitive impairment (MCI), a combination of PD and MCI and subjects belonging to the control group of healthy individuals. For pre-processing and analysis, the MATLAB environment, the SPM12 toolbox and The Brain Connectivity Toolbox were used.
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Manifestation of physiological noise in fMRI data
Skoupý, Radim ; Mareček, Radek (referee) ; Lamoš, Martin (advisor)
In this bachelor thesis I deal with the manifestations of physiological noise in fMRI data. The work includes the basic theory of BOLD signal - his character, dealing with the processing of measured data, the possibilities of their treatment, filtration and formation of the resulting statistical parametric maps. The key part is studing possibilities of physiological noise filtering method Retroicor that models physiological noise based on sine and cosine basis functions.
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Simultaneous EEG/fMRI analysis using EEG data processing
Ištok, Martin ; Vítek, Martin (referee) ; Lamoš, Martin (advisor)
The main objective of this diploma thesis is to describe simultaneous electroencephalography-correlated functional magnetic resonance imaging analysis using EEG data processing. It includes basic characteristics of EEG and fMRI recording and analysis and their combination as simultaneous EEG/fMRI analysis and deals with obstructions during its processing. The thesis includes a design of an experiment used for recording and analysis of simultaneous EEG/fMRI data using EEG source reconstruction for regressor construction. Thesis incorporates a software solution used for extraction of signal describing a source activity interpolated by EEG source reconstruction. The signal is then processed and used to construct a basic regressor. The thesis also deals with the software solution being used for a study focused on intracranial epileptic discharges localization using a simultaneous EEG/fMRI analysis in which it reveals source activity during ongoing epileptic spike and summarizes the results.
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X-ray projection imaging- model of structural noise suppression
Lamoš, Martin ; Kolář, Radim (referee) ; Drastich, Aleš (advisor)
The aim of this task is to create a program that will simulate noise components and methods of their elimination for X-ray projection imaging with focus on structural noise. MATLAB has chosen as the environment for the implementation. Some of the toolboxes shipped with MATLAB has also been used, mainly the Image Processing Toolbox. The methods and elements are implemented as independent functions, which are highly configurable through the setting of the input parameters. All of functions are covered in a custom application. The model is become user friendly and it is suitable teaching support as a laboratory task. The methods it is possible to use for the structural noise suppression are: temporal image subtraction, temporal integration, matched filtration and recursive filtration. There are three methods of cumulation for physical noise suppression. With proper settings it is possible to suppress also the periodical motional noise suppression.
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Segmentation of blood-vessel tree in whole-body MRI data
Guricová, Karolína ; Lamoš, Martin (referee) ; Kolář, Radim (advisor)
Práce popisuje anatomii a vlastnosti cévního eit s charakteristickými znaky, na kterých je zaloena jeho segmentace. Nejprve jsou uvedeny metody segmentace 3D CT a MRI sken. Více detailn jsou popsány základy segmentace zaloené na druhých derivacích a Hessov matici. K urení podobnosti cévám v pvodním obraze jsou spoítány vlastní ísla Hessovy matice kadého voxelu. K vytvoení výsledného segmentovaného obrazu je navreno více metod pro zpracování tchto vlastních ísel. Metoda je prakticky implementována v MATLABu. Vysegmentované arteriální eit je visualizováno pomoc í knihovny VTK kódované v Pythonu. Dále je navreno GUI, které umouje mení v zpracovaném objemu. Délky artérií jsou aproximovány lineárními úseky kopírujícími jejich cesty a výsledky tohoto mení jsou v práci prezentovány. Limitace této metody a návrh na poloautomatické mení jsou rozebrány na konci této práce.
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Detection of blood elements
Kadlček, Václav ; Kolář, Radim (referee) ; Lamoš, Martin (advisor)
Thesis deals with the detection and subsequent blood elements classification. Blood elements are described mainly in terms of optical features, that is used for digital image processing. Furthermore, available pre-processing theory, image analysis and methods of classifikation are discussed. Acquired knowledges are applied in MATLAB. Image Processing Toolbox is a pillar for that work within this programming environment. The program includes user interface, thus facilitating communication with the program. The program was tested on blood smear images and the results were evaluated.
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MRI image segmantation based on edge detection
Simichanidis, Michail ; Lamoš, Martin (referee) ; Harabiš, Vratislav (advisor)
Cílem této práce je představit základní segmentační techniky používáné v oblasti medicínského zpracování obrazových dat a pomocí 3D prohlížeče schopného zobrazit 3D obrazy implementovat segmentační modul založený na hranové detekci a vyhodnotit výsledky. Navrhovaný prohlížeč je sestavený v prostředi Matlab GUI a je schopen načíst objem 3D snímků představující lidskou hlavu. Navrhovaný segmentační modul je založen na použití hranových detektorů, zejména Cannyho detektoru.
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