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Compressed sensing in magnetic resonance perfusion imaging.
Mangová, Marie ; Veselý, Vítězslav (referee) ; Rajmic, Pavel (advisor)
Magnetic resonance perfusion imaging is a today's very promising method for medicine diagnosis. This thesis deals with a sparse representation of signals, low-rank matrix recovery and compressed sensing, which allows overcoming present physical limitations of magnetic resonance perfusion imaging. Several models for reconstruction of measured perfusion data is introduced and numerical methods for their software implementation, which is an important part of the thesis, is mentioned. Proposed models are verified on simulated and real perfusion data from magnetic resonance.
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Neuroinformatics: calibration methods in multicentric MR studies
Kovalčík, Tomáš ; Říha, Ivo (referee) ; Provazník, Ivo (advisor)
Work deals with methods of calibration of multi-center study of magnetic resonance imaging. Magnetic resonance is the phenomenon of the substance in a magnetic field of induction B0 delivers energy in the form of RF pulse with the Larmor frequency and thus to excite particles to higher energy levels. Calibration can be performed using the distinctive and homogeneous RF phantoms. Furthermore, we can perform calibration using image registration. To calibrate the images by registering the work described in the classical linear (affine) and nonlinear. Listed below are the simulators, which are also useful for modeling various artifacts.
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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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Emerging Trends in Dendrochronology
Horáček, Tomáš ; Neuwirthová, Ludmila (referee) ; Mikulka, Jan (advisor)
Tato práce se zabývá popisem současných a experimentálních metod odběru vzorků pomocí presslerova nebozezu, výřezů z kmene, fotografie, rentgenu, počítačové tomografie a magnetické rezonance na poli dendrochronologického výzkumu. V práci jsou rozebírány destruktivní a nedesktruktivní metody odběru vzorků. Je také kladen důraz na původ vzorků: zdali je možno využít destruktivní metody nebo zdali je to nemožné jako v případě vzácných archeologických objektů. Dále popisuje standardní optometrickou metody a další experimentální metody fungujicí na principu kontranstního zpracování obrazu za účelem rozeznání letokruhů. V práci jsou také popsány různé druhy metod softwarového zpracovnání kde jako vstup slouží buď série dat nebo obraz letokruhů. Další rozdíly tvoří vymezené spektrum uvedených prací, některé práce se zaměřují na zpracování obrazu od píky tedy od pořízené fotografie až po hotové datovaní, některé však zajímá pouze úzký sektor dendrochronologie jako jsou například vady či špatně rozeznatelné letokruhy.
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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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Scaling of arterial input function in DCE-MRI
Holeček, Tomáš ; Kolář, Radim (referee) ; Kratochvíla, Jiří (advisor)
Perfusion magnetic resonance imaging is modern diagnostic method used mainly in oncology. In this method, contrast agent is injected to the subject and then is continuously monitored the progress of its concentration in the affected area in time. Correct determination of the arterial input function (AIF) is very important for perfusion analysis. One possibility is to model AIF by multichannel blind deconvolution but the estimated AIF is necessary to be scaled. This master´s thesis is focused on description of scaling methods and their influence on perfussion parameters in dependence on used model of AIF in different tissues.
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Use of nanofluidic mixing for preparation of liposome carriers stained by gadolinium for contrast imaging by magnetic resonance (MRI)
Velínská, Kamila ; Mašek,, Josef (referee) ; Turánek, Jaroslav (advisor)
This diploma thesis focuses on the preparation of the liposomes, containing lipids with gadolinium, which are used for a contrast magnetic resonance imaging. The liposomes were prepared by the lipid film hydration followed by an extrusion and also by a new nanofluid mixing method on the NanoAssemblr Benchtop. The preparation technology has been optimized for parameters such as the composition of lipids, the flow rate ratio and total flow rate. The method of modification of the liposomes surface by gadolinium complexes has been developed. This method is using a conjugation reaction between the lipids containing cyanuric acid and Gd-DOTA. Prepared Gd-liposomes, which contain gadolinium, were complexly defined by the characterization techniques of DLS and NTA. The morphology of liposomes was observed by TEM and cryo-TEM. Methods for the determination of phospholipid content (Stewart test) and residual water in the lyophylisates of liposomes (Karl-Fischer titration) were used. Gadolinium in liposomal preparations was determined by ICP-OES. Using MR, the concept of gadolinium liposomes was verified and designed for MRI imaging of thrombi. The concept describing the mechanism of liposomes formation based on the experimentally proven existence of a phospholipid bilayer fragment has been developed. This concept is based on the experimentally proven existence of a phospholipid bilayer fragment.
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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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Wavelet analysis and enhancement of MR tomography and ultrasound images
Matoušek, Luděk ; Bartušek, Karel (referee) ; Smékal, Zdeněk (advisor)
Tomographic MR (Magnetic Resonance) and sonographic biosignal processing are important non-invasive diagnostic methods used in a medicine. A noise added into processed data by an amplifier of tomograph receiving part and by circuits of sonograph is resulting in a body organ diagnosis degradation. Image data are stored in a standardized DICOM medical file format. Methods using wavelet analysis for noise suppression in image data have been designed and their comparation with classical methods has been made in this work. The MATLAB was utilized for data processing and data rewriting back to the DICOM format.
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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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