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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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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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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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Calculation of advanced diffusion parameters in brain grey matter from DKI MRI images
Pánková, Olga ; Jakubíček, Roman (referee) ; Minsterová, Alžběta (advisor)
Thesis named Calculation of advanced diffusion parameters in brain grey matter from DKI MRI images deals with processing of diffusion-weighted images from DKI. The thesis contains review of literature on principle of diffusion, influence of diffusion on MRI, calculation of DTI and DKI parameters and clinical application of diffusion-weighted maps with focus on grey matter. The thesis focuses on software tools for processing and pre-processing DTI and DKI. The practical part consisted of two sections. Two different softwares were used to calculate maps of diffusion parameters. Diffusion parameters from anatomical structure sunstantia nigra were compared between group of healthy controls and patients with Parkinson’s disease. This comparison did not show any statisticaly significant difference. In the second step, a script for creating diffusion maps in software Diffusinal Kurtosis Estimator was made.
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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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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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Structural Patterns of Cognitive Deficits in MR Imaging.
Buksakowska, Irena ; Hořínek, Daniel (advisor) ; Rulseh, Aaron (referee) ; Dušek, Petr (referee)
Structural and diffusion imaging patterns that can be evaluated using MRI in patients with cognitive deficits are the central theme of the proposed work. First, the clinical and neuroimaging background of dementias has been reviewed in a broader context, with a special focus on Alzheimer's disease (AD) and differential diagnoses. The second part of this thesis contains four consecutive experimental studies. The primary objective of the first two studies was to obtain structural and microstructural information on the neurodegenerative processes characteristic for AD on global and regional levels. For this purpose, several complementary approaches were used and the focus was shifted from grey to white matter (GM/WM). The following two studies focused on the differential context of WM microstructural alterations in normal pressure hydrocephalus (NPH) and distinctive patterns of WM disintegrity in temporal lobe epilepsy (TLE). The most important conclusion of our studies is that structural and diffusion imaging proved to be useful in identifying regionally specific and disproportionate loss of brain volume and microstructure in several pathological processes underlying cognitive deterioration. The use of distinctive morphometric methods yielded complementary information on AD-related atrophy patterns,...
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Calculation of advanced diffusion parameters in brain grey matter from DKI MRI images
Pánková, Olga ; Jakubíček, Roman (referee) ; Minsterová, Alžběta (advisor)
Thesis named Calculation of advanced diffusion parameters in brain grey matter from DKI MRI images deals with processing of diffusion-weighted images from DKI. The thesis contains review of literature on principle of diffusion, influence of diffusion on MRI, calculation of DTI and DKI parameters and clinical application of diffusion-weighted maps with focus on grey matter. The thesis focuses on software tools for processing and pre-processing DTI and DKI. The practical part consisted of two sections. Two different softwares were used to calculate maps of diffusion parameters. Diffusion parameters from anatomical structure sunstantia nigra were compared between group of healthy controls and patients with Parkinson’s disease. This comparison did not show any statisticaly significant difference. In the second step, a script for creating diffusion maps in software Diffusinal Kurtosis Estimator was made.
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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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