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Noise and artifact suppression in fMRI data based on multi-echo data and independent component analysis
Pospíšil, Jan ; Gajdoš, Martin (referee) ; Mikl, Michal (advisor)
The main task of this work is to design an algorithm for suppressing unwanted noise and artifacts in fMRI data using the analysis of independent components and multi-echo data. The theoretical part deals with the basic principles of magnetic resonance, including construction and image data processing. The practical part presents a pilot design of a method inspired by a professional publication in the Matlab software environment, where this design is subsequently tested on real fMRI data provided by the Laboratory of Multimodal and Functional Imaging, CEITEC MU.
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Similarity/dissimilarity analysis of genomic data on the basis of graphical representation
Těthal, Jiří ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
The work deals with the identification of species of animal through the density of nucleotids of mitochondrial gene CO1. In the first part the theory summarized information about DNA barcoding and the mitochondria, cellular organel that with this method is closely related. The second part deals with virtually comparing different sequences using the density of nucleotides. For this it was created program, which uses two functions, the first of the specified nucleotide sequence calculates the density and one can compare the density by distance methods.
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Fuzzy classification of DNA sequences
Těthal, Jiří ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
The work deals with the fuzzy classification of DNA sequences. In the first part the theory summarized information about Fuzzy logic and methods of its use in the classification of biological sequence data. The second part is practically deal with the classification algorithm for assessing the similarity of sequences. Specifically, the dividing of coding and non-coding parts of the sequence and the use of fuzzy classification in DNA barcoding.
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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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Live typeface
Jiříček, Milan ; Špiřík, Jan (referee) ; Rajmic, Pavel (advisor)
The work describes the theoretical foundations of modern methods of creating new fonts, that is, using information technology, specifically vector programs. It also marginally shows the history of the font, Roman writing, the basic division of its compositions and describes its individual elements. The next part of the project focuses on creating digital fonts and continues with bringing it to live using algorithms and methods that can easily be processed in Matlab programming language. The method of implementation of the bringing the typeface to live is described and presentation of the generated results are then shown in few examples. Attention is also paid to the coordinates system, which is very important to solve geometric transformations, and two-dimensional vector graphics, which are widely used in the design and to render the fonts. Bézier curves and cubic Bézier curves are described in further detail along with vector graphics rasterization. One part of this text describes very important de Casteljau algorithm. The last chapter focuses on implementation in Matlab programming language, the creation of curves, that means single font characters, and the ways of how the algorithm works with transformations. Some sample images showing transformations using different input arguments are displayed in this section as well. There is evaluation of the contribution of this application and the possibilities of further expansion at the end.
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Visualization and export outputs from functional magnetic resonance imaging
Přibyl, Jakub ; Gajdoš, Martin (referee) ; Slavíček, Tomáš (advisor)
Thesis discusses the principles and methodology for measuring functional magnetic resonance imaging (fMRI), basically the origin and use of BOLD signal types used experiments. Further attention is paid fMRI data processing and statistical analysis. Subsequent chapters are devoted to a brief description of the most common software tools used to analyze data from fMRI. The main section was to create a program in MATLAB with a detailed graphic user interface for easy visualization and export output from analyzes of fMRI data. The second half is devoted to describing the program developer and graphic user interface, including key functionality. The final section describes the application program with real data from clinical studies of dynamic connectivity and use in an international project APGem.
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Hemodynamic model in effective brain connectivity analysis using fMRI
Holeček, Tomáš ; Harabiš, Vratislav (referee) ; Lamoš, Martin (advisor)
Modeling of hemodynamic response based on changes of synaptic activity is used for mapping active areas of the brain or functional organization of the brain using functional magnetic resonance imaging. Hemodynamic model is one of the methods for modeling hemodynamic response. Balloon model is the main part of the hemodynamic model. Hemodynamic model is used in the mapping active areas using general linear model and in the effective brain connectivity analysis using dynamic causal modelling. This bachelor´s thesis is focused on description of the hemodynamic model, its parameters and impact of every single parameter of the hemodynamic model on its response.
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A comparison of effective and functional connectivity methods in fMRI
Gajdoš, Martin ; Schwarz, Daniel (referee) ; Jan, Jiří (advisor)
Functional magnetic resonance imaging (fMRI) is recent important method, used in neuroimaging. The aim of this thesis is to develop software tool for comparison of two methods for functional and effective connectivity estimation. In this thesis are described the basics of magnetic resonance imaging, fMRI, basic terms of fMRI experiments and generally are described methods of functional and effective connectivity. Then are more detailed mentioned methods of dynamic causal modeling (DCM), Granger causal modeling (GCM) and independent component analysis (ICA). Practical implementation of DCM in toolbox SMP and ICA in toolbox GIFT is also mentioned. In purpose to describe behavior of DCM and GCM in dependence on several parameters are performed Monte Carlo simulations. Then the concept and realization of software tool for simulating connectivity and comparison of DCM and GCM are described. Finally results of DCM and GCM comparison and results of Monte Carlo simulations are discussed.
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Influence of the reaction time on neuronal response amplitude after the uncommon stimuli in fMRI images
Klimeš, Filip ; Bartoň, Marek (referee) ; Lamoš, Martin (advisor)
The goal of my bachelor’s thesis is to provide basic idea of the functional magnetic resonance imaging. The theoretical part deals with general principles, methods of measurement and analysis of fMRI data. The partial and also key objective is to design ways of modelling reaction time within the concept of general linear model. The goal of the practical part was to become familiar with SPM toolbox and then to implement designed ways on group data. The implementation was carried out at two levels: preprocessing and analysis of measured data. Preprocessed data were subjected to the first level analysis and second level analysis. Next aim is to evaluate the results of both analysis and thus different approaches to the modelling of reaction time and its influence on neuronal response amplitude after uncommon stimuli in functional magnetic resonance images.
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