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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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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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Application of Diffusion Tensor Imaging to Brain Gray and White Marker
Rulseh, Aaron Michael ; Vymazal, Josef (advisor) ; Hluštík, Petr (referee) ; Hájek, Milan (referee)
Application of Diffusion Tensor Imaging to Brain Gray and White Ma er A In the present work we explore the gray and white ma er applicability of diffusion tensor imaging (DTI). To evaluate effect of ferritin-bound iron on gray ma er contrast in DTI, we created an in vitro model consisting of agarose gel phantoms doped with ferritin, and validated our results in vivo on healthy volunteer subjects - years of age in the basal ganglia. We further explored the application of DTI to amyotrophic lateral sclerosis (ALS) and multiple system atrophy (MSA); neurodegenerative diseases with gray and white ma er pathophysiological components. In the ALS study, patients and age- and sex-matched controls were recruited, while the MSA study included probable MSA subjects ( MSA-P, MSA-C) and age- and sex-matched controls. We found that ferritin-bound iron may make a signi cant contribution to DTI scalars in gray ma er regions of the brain, mediated by eigenvalue repulsion. is has important implications for DTI studies targeting gray ma er regions, especially in adolescence and in diseases associated with altered brain-iron load. In ALS, we found altered diffusion in the corona radiata and callosal body, and changes in R in the caudate nucleus and frontal white ma er. In MSA, we observed widespread white ma er changes associated...
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Dopady regulací na trh spotřebitelských úvěrů na bydlení
Vinklárek, Filip
Diploma thesis focus on the regulation of consumer housing loans market. Based on the analysis of the consumer housing loans market in the European Un-ion, the main regulations and factors affecting this market are identified. Panel data analysis is available to determine the effects of regulation and factors on mortgage lending. The explained variable is the growth of mortgage loans. The explanatory variables are macroeconomic factors and macroprudential policy in-struments. Results showing effects of macro-prudential instruments on the con-sumer housing loans market.
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Vyhodnocení dopadu doporučení ČNB na spotřebitele využívajícího účelového úvěru na bydlení
Benáček, Aleš
Goal of this thesis is to gain perspective on the change of situation of con-sumer that uses loans purposed for securing own housing based on recom-mendations by Czech National Bank for providers of these loans. In order to achieve this goal, author will use method of description to sum-up the theo-ry and current situation on the loan market. In the next part, author will try to simulate the situation of the household of two consumers with income on the level of median wage, which wants to use the housing-purposed loan, and how its ability to take certain amount of money and its purchasing power have changed in the last five years. Author will interpret findings of his empirical analysis and suggest possible solution which could improve current state of the matter.
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HARDI dMRI Imaging Of Cervical Spinal Cord
Zimolka, Jakub ; Piskořová, Zuzana ; Svátková, Alena ; Bednařík, Petr ; Horák, Tomáš ; Hok, Pavel
Our work established an automatic pipeline of cervical spinal cord high angular resolution diffusion imaging (HARDI) data. Our pipeline that projects the diffusion results into high-resolution anatomical space utilizes Spinal Cord Toolbox (SCT), FSL libraries, in-house developed scripts and TORQUE-based batch system for grid computational engines. As one of the first, we are investigating multiple-direction models for human in-vivo spinal cord HARDI dMRI data. The visually inspected preliminary results indicate that significant 2nd directions are observable as expected based on previously presented mainly animal models. Our work provides an essential clinical tool that will allow quantifying spinal cord and dorsal spinal roots alterations in various neurological diseases in vivo.
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Application of Diffusion Tensor Imaging to Brain Gray and White Marker
Rulseh, Aaron Michael ; Vymazal, Josef (advisor) ; Hluštík, Petr (referee) ; Hájek, Milan (referee)
Application of Diffusion Tensor Imaging to Brain Gray and White Ma er A In the present work we explore the gray and white ma er applicability of diffusion tensor imaging (DTI). To evaluate effect of ferritin-bound iron on gray ma er contrast in DTI, we created an in vitro model consisting of agarose gel phantoms doped with ferritin, and validated our results in vivo on healthy volunteer subjects - years of age in the basal ganglia. We further explored the application of DTI to amyotrophic lateral sclerosis (ALS) and multiple system atrophy (MSA); neurodegenerative diseases with gray and white ma er pathophysiological components. In the ALS study, patients and age- and sex-matched controls were recruited, while the MSA study included probable MSA subjects ( MSA-P, MSA-C) and age- and sex-matched controls. We found that ferritin-bound iron may make a signi cant contribution to DTI scalars in gray ma er regions of the brain, mediated by eigenvalue repulsion. is has important implications for DTI studies targeting gray ma er regions, especially in adolescence and in diseases associated with altered brain-iron load. In ALS, we found altered diffusion in the corona radiata and callosal body, and changes in R in the caudate nucleus and frontal white ma er. In MSA, we observed widespread white ma er changes associated...
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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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