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Tool for analysis of subject's movements in functional magnetic resonance measurements.
Šejnoha, Radim ; Lamoš, Martin (referee) ; Gajdoš, Martin (advisor)
This diploma thesis deals with an analysis of subject’s movement during measurements with funcional magnetic resonance imaging (fMRI). It focuses on methods of a movement artifacts detection and their removal in fMRI images. Thesis deals with metrics which are used for the movement rate of measured subjects evaluation. Metrics and a correction of movement are implemented into the programme in MATLAB. Comparison of subjects suffering from Parkinson’s disease with a group of healthy control was carried out. Tresholds of individual metrics were suggested and a criterion for the removal of subjects with high movement rate was determined.
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Application of Interferometry in VT UHV SPM
Šulc, Dalibor ; Klapetek, Petr (referee) ; Fejfar, Antonín (referee) ; Spousta, Jiří (advisor)
The thesis is aimed at the development of Scanning Probe Microscopes (SPM). It describes design and development of modular controll electronics to be applied eectively on more microscopes SPM. Control electronics consist of stabilized power source, high–voltage amplier and probe signal amplier. The open–source project GXSM has been introduced. It contains a logic control unit which controls scanning, acquiring data and feedback control. GXSM provides a graphical user interface based on linux operation system. Second part of the thesis is aimed at design and development of interferometric deection sensing system for SPM cantilevers and applications at SPM in general. Designed interferometer has been assembled and tested. It can clearly distinguish a signal of amplitude 2 nm. At the end of the thesis the design of interferometric system implementation is presented.
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Design of Low-Temperature Ultra High Vacuum Scanning Probe Microscopes
Pavera, Michal ; Klapetek, Petr (referee) ; Vetushka, Aliaksei (referee) ; Šikola, Tomáš (advisor)
This thesis deals with the development of scanning probe microscopes. Mechanical requirements for microscopes using measuring methods of scanning tunneling microscopy (STM) and atomic force microscopy (AFM) under enviroments of an ultrahigh vacuum (UHV) and variable temperatures are specified. Mechanical designs of two microscopes are discussed and their control electronics described. A special chapter is devoted to description of linear piezo manipulators and mechanical design of these prototypes.
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Study of Properties of Metallic Thin Films and Nanostructures Using Scanning Probe Microscopy
Doupal, Antonín ; Fejfar, Antonín (referee) ; Kalousek, Radek (advisor)
This diploma thesis is focused on investigation of metallic thin films and nanostructures using scanning probe microscopy. Magnetic properties of these objects are studied by magnetic force microscopy, which is modification of scanning probe microscopy. In the theoretical part basic principles of scanning probe microscopy and magnetic force microscopy are summarized, and also principle of creation of magnetic domains and some special properties of ferromagnetic and antiferromagnetic materials. Further, two techniques of fabricating nanostructures are described. Experimental part is focused on imaging and simulating of magnetic domains. Further, exchange bias is revealed. This phenomenon is present in systems composed from ferromagnetic and antiferromagnetic materials. One part of this diploma thesis is also focused on discussion of problems with magnetic force microscopy.
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Aplication of SPM in study and modification of ultrathin films Pt, Co and graphene
Lišková, Zuzana ; Červenka,, Jiří (referee) ; Bartošík, Miroslav (advisor)
This diploma thesis deals with the preparation of the very thin films and their investigation by scanning probe microscopy methods. The ultrathin films of Pt on Pt(111) were created by pulsed laser deposition and the ultrathin films of Co on Pt(111) were deposited by thermal evaporation. The coverage of the substrate was much smaller than one monolayer (in order of hundredths of monolayer). The nucleation theory was verified by these experiments using so-called Onset method. Further graphene sheets were prepared on layer of Si/SiO2 by the mechanical exfoliation from the graphite crystal. The fabricated graphene sheets were studied by micro-Raman spectroscopy, microreflectometry, atomic force microscopy and similar techniques. These methods proved the thinnest graphite layers were consisted of two graphene monolayers.
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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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The Use of AFM Measurement Method in Crystalline Silicon Solar Cells Technology
Mojrová, Barbora ; Boušek, Jaroslav (referee) ; Hégr, Ondřej (advisor)
This thesis deals with the use of Atomic Force Microscopy (AFM) and Kelvin Probe Force Microscopy (KPFM) in solar cells production. Both techniques measure surface properties using interactions between surface and tip that progressively scans entire surface of the sample. Atomic force microscopy allows three dimensional imaging of surface structure. Kelvin probe force microscopy is used to measure the contact potential difference on the sample surface. There are described experimental measurements of monocrystalline and multicrystalline substrates after various etching processes using AFM. By using KPFM the contact potential difference was measured on dielectric layers PSG, SiOX, SiNX and Al2O3 and on selective emitter structures. All experiments described in this work were carried out at the Solartec Ltd. workplace and they completely correspond with the actual technology of crystalline solar cells production.
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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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Non-linear character of optical environment
Žáček, Martin ; Míča, Ivan (referee) ; Přinosil, Jiří (advisor)
This paper describes theoretical and application options of nonlinear effects in optical medium. Optical medium means fiber optics, because the fiber is the most employed optical medium at these days. Basic statements of this work are theoretical information with mathematical and physical expressions. These expressions defines nonlinear medium and effects which are founded here. These effects are split to second and third orders. Nonlinear effects of second orders are Second-harmonic Generation, Three-wave Mixing process. Nonlinear effects third orders are Third-harmonic Generation, Self-phase Modulation, Cross-phase Modulation, Four-wave Mixing and Degenerative Four-wave Mixing process. These effects are extended by scattering effects – Brillouin’s and Raman‘s Scattering. The next point discuss about optical communication system DWDM. DWDM uses dense wavelength multiplexing. Nonlinear effects have a few negative influences on these systems. There are requests for high bandwidth and communication speed. FWM and XPM limit these requests. They can invoke cross-talks. We support theoretical information with application examples and simulations at the end of this work. We use OptSim v.4.0 program. We are simulate FWM and XPM effect in depend on chromatical dispersion and power.
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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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