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Trainable image segmentation using deep neural networks
Majtán, Martin ; Burget, Radim (referee) ; Harár, Pavol (advisor)
Diploma thesis is aimed to trainable image segmentation using deep neural networks. In the paper is explained the principle of digital image processing and image segmentation. In the paper is also explained the principle of artificial neural network, model of artificial neuron, training and activation of artificial neural network. In practical part of the paper is created an algorithm of sliding window to generate sub-images from image from magnetic rezonance. Generated sub-images are used to train, test and validate of the model of neural network. In practical part of the paper si created the model of the artificial neural network, which is used to trainable image segmentation. Model of the neural network is created using the Deeplearning4j library and it is optimized to parallel training using Spark library.
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Volume Rendering Using Programmable HW
Jošth, Radovan ; Kršek, Přemysl (referee) ; Herout, Adam (advisor)
This work describes and implementing method for volume data rendering. Main purpose of this work is visualization of scanned 3D data with some current method used for the 3D volumetric scanning. The 3D volumetric scanning is mainly used in medicine and chemistry. System is using programmable pipeline of current graphic cards, which provides us fast parallel work with large volumetric data. This paper introduces some basics about the volumetric rendering and scanning, describes design and at the end, the implementation steps. Result of this project is application which renders volumetric data with OpenGL.
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MRI Data Processing Acceleration on GPU
Kešner, Filip ; Nečas, Ondřej (referee) ; Polok, Lukáš (advisor)
This BSc Thesis was performed during a study stay at the Universita della Svizzera italiana, Swiss. The identification of trajectories of neuron fibres within the human brain is of great importance in many medical applications as the neural diagnostics, neuronavigation, treatment of epilepsy, surgical removal of tumors and etc. By using diffusion MRI-data as input, and by employing Monte-Carlo like methods, possible trajectories are generated and the most likely ones can be visualized. These can serve as input for advanced medical diagnosis and treatments. Due to the huge amount of data to be analyzed and many iterations, this is a time consuming process. For the purposes such as statistical analysis and comparsion over several datasets or several patients, computational time requirements are enourmous. Faster diagnosis can improve routine throughput and provide earlier treatment of illness. At this time, there exists only a very few implementations of neural tractography sof tware. For probabilistic neural tractography is the list of software even thiner. Today's implementations using standard serial CPU execution suffer from high time consumption. The goal is to provide an efficient implementation which makes use of GPGPUs and exploits parallelism in the method. For the GPU implementation, a comparsion of CUDA and OpenCL technologies will be provided, using the more suitable one.
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Simulation of synthetic diffusion tensor data
Labudová, Kristýna ; Mézl, Martin (referee) ; Labounek, René (advisor)
This work deals with different approaches to imaging of diffusion intensity with magnetic resonance. Individual approaches are described and compared. Gaussian model for approximation of diffusion profile is analysed and mathematically determined in details. The next part of this work concerns about process of simulation synthetic diffusion tensor data, adding noise to data and estimation of diffusion tensor from noisy data. Estimation’s accuracy is rated according to deviation of fractional anisotropy of estimated and original tensor and also according to deviation of the main eigenvectors of both tensors. Accuracy of the estimation is evaluated automatically with the programme. There is realization of graphical interface for simulation as well as for automatical evaluation of results described in details. At the end of this work all results are processed and commented and there is also recommendation for optimal adjustment of the data acquisition. 120 gradient directions are the most optimal of all analysed direction. It provides sufficient accuracy of results with optimal time of data acquisition which is suitable for clinical praxis.
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MRI compatible optic fiber thermometer
Stibůrek, Miroslav ; Čučka, Milan (referee) ; Harabiš, Vratislav (advisor)
The following work deals with basics of fiber optics, history of fiber optics, and methods of measuring physical quantities with the use of fiber optic sensors. The work includes facts about physics, chemistry and biology - these elements are necessary for a full understanding of the issue. In order to create an optical fiber temperature sensor based on Fabry Perot resonator principle, several methods of manufacturing the optical cavity are investigated. A practical part of paper consist in the manufacturing of the miniature fiber thermometer, its coating and testing.
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Multi-tensor imaging of spinal cord detail from high anglular resolution dMRI data
Zimolka, Jakub ; Starčuk, Zenon (referee) ; Labounek, René (advisor)
The aim of this work was to establish a comprehensive processing pipeline of cervical spinal cord HARDI dMRI data and T2-weighted anatomical MRI images in high-resolution. In the research part we provide description of anatomical data processing, theoretical background of dMRI, description of current approaches to 3D anisotropic diffusion estimation as well as current imaging methods of spinal cord axonal bundles. As one of the first in the world, we are investigating multiple-direction diffusion models for human in-vivo spinal cord white matter minority bundles imaging. We designed our own processing pipeline utilizing Spinal Cord Toolbox (SCT), FSL, in-house developer scripts and TORQUE-based batch system for grid computation, tested on real data from cervical spinal cord area between segments C4-C6 from 26 healthy volunteers. Designed processing pipeline with one non-automatic step, works from pre-processing to parcelation of selected spinal cord structures based on co-registration with anatomical spinal cord template for 25 subjects. One person data includes motion artifacts for which the proces failed. There are visible waves in sagittal images of some subjects caused probably by blood-vessel pulsing. Local quantification metrics of spinal cord anatomy (fractional anisotropy – FA, fractional volumes of first – f1 and second – f2 direction of anisotropic diffusion) from different parts (white matter, gray matter, cortico-spinal tract) and from different population groups (men vs. women), were extracted from dMRI data. As we expected, FA maps show visible decreases in areas of gray matter. We also detected second diffusion dirrection in slices, where the spinal roots come out. In some areas, fractional volume of second diffusion direction reaches up to 40% of the total component of the dMRI signal. All mentioned parameters probability density functions for all mentioned groups are non-normal distributions. Between male and female groups there were no significant distribution differences for f1 and f2 volumes. The distribution of FA values between men and women is statistically different. Unfortunatelly, there is a significant inter-subject variability in results, which has much higher dispersion than differences between different group distributions. Despite the inter-subject variability, this work significantly extends the knowledge about data acquisiton capabilities and MRI and dMRI data from cervical spinal cord image processing. This work also lays down foundations for utilization of the imaging method in future and planned clinical research, where it will be possible to test the alteration of the spinal cord anatomy on the minor secondary bundles separately.
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Neuroinformatics and sharing data from medical imaging systems
Klimek, Martin ; Kubásek, Miroslav (referee) ; Provazník, Ivo (advisor)
The presented master's thesis deals with the issue of storing and sharing data from medical imaging systems. This thesis, inter alia, consists of organizational and informatics aspects of medical imaging systems data in multicentric studies containing MRI brain images. This thesis also includes technical design of a web-based application for image data sharing including a web interface suitable for manipulation with the image data stored in a database.
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Fixation of the biological samples
Brachtl, Martin ; Jiřík, Radovan (referee) ; Krátká, Lucie (advisor)
The aim of thesis is acquaint with possibilities of fixation biological tissues. Choose a suitable tissue and fix it with formaldehyde and another fixator. Last but not least make measurements which determine effects of formaldehyde on the relaxation time of biological tissues. Mice brains were chosen as a suitable for tissues fixation. Measuring effects of formaldehyde and another fixator to relaxation time carried out at the Institute of Scientific Instuments Academy of Sciences of the Czech Republic.
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RF coil for MR systém
Vojtíšek, Miloš ; Kořínek, Radim (referee) ; Gescheidtová, Eva (advisor)
The bachelor thesis is focused on radio frequency coils for magnetic resonance imaging systems. Magnetic resonance is used for imaging of many objects, especially human body in medicine, plants and many other different objects. For obtaining optimal results it is essential to use a special suitable coil for every single application. In the first part of this work, the short overview of principles of magnetic resonance imaging is described followed by a look at hardware used in MRI. The main aim of the work is design of several different types of RF coils used in MRI. Finally two suitable designs have been chosen for the purpose. Coils have been realized, tested in experiments. Results were analyzed, maps of generated magnetic field were calculated and homogeneity was determined.
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Development of Imaging Methods and its Importance to Biomechanics
Sedláček, Tomáš ; Houfek, Martin (referee) ; Florian, Zdeněk (advisor)
The main objective of this bachelor thesis is to collect all available literature, from which can reader obtain basic knowledge of imaging methods. The methods are divided by its origin into four categories: x-rays, magnetic resonance, ultrasound and nuclear medicine. Each of them is described from the historical, physics and technological view. At the end the importance of each method to medicine and biomechanics is summarized.
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