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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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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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Diffusion Tensor Measurement
Hrmel, Martin ; Steinbauer, Miloslav (referee) ; Bartušek, Karel (advisor)
The aim of this bachelor thesis is to create methodology for measuring diffusion tensor using MR and experimental verification on chosen biological sample. A set of samples was measured. At first, diffusion of the set of samples was evaluated, then diffusion tensors was evaluated on onion's sample by using programs Marevisi and Matlab. To obtain image a magnetic resonance was used.
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Tracking of Axonal Bundles in Diffusion MRI Brain Images
Piskořová, Z.
The aim of this work is to design tracking algorithm which will be able to track brain axonal bundles in diffusion weighted MRI data. Estimation of anisotropic diffusion profile inside voxels was performed by diffusion tensor imaging model (DTI). Tracing is based on the 4th order Runge-Kutta method. Algorithm is implemented in the MATLAB computing environment and is tested on real data biological phantom.
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SMV-2014-22: Development of magnetic-resonance methodology for research into Parkinson’s disease in an animal model
Starčuk jr., Zenon
Collaborative development of an animal model of Parkinson’s disease, design and optimization of a suitable set of MR measurements, measurement of sample animals provided (40 mice, anatomy+diffusion), data adaptation for hand-over. The work was focused to the verification of a transgenic mouse model of Parkinson’s disease and the development of an optimal protocol for anatomic MRI of the mouse brain, with an emphasis on the regions of substantia nigra, hippocampus, striatum and on the comparison between the diagnostic values of DTI and DKI measurements in these regions. Experimental data were individually analyzed for each mouse and statistically evaluated in groups of test and control animals. Based on pathophysiology assessment further MR procedures were suggested for patophysiology research and the development of early diagnostics and therapy monitoring.
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