|
|
Reverse Monte Carlo as MRS quantitation quality assessment
Jabłoński, Michal ; Starčuková, Jana ; Starčuk jr., Zenon
Data analysis of Magnetic Resonance Spectroscopy (MRS) using quantitation algorithms, such as AQSES, QUEST, AMARES or LCModel produces estimates of relative metabolite concentrations and their precision, estimated as the Cramer Rao Lower Bounds (CRLB). This assessment does not guarantee the uniqueness of the fit, and thus is not a true representation of the concentration uncertainty. In this publication authors propose to verify the quality of fitting by Reverse Monte Carlo method, which is independent of the estimator and has weaker requirements on the solution and model accuracy.
|
|
|
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.
|
|
| |
|
| |
|
| |
|
|
MR imaging of fluorine-19
Meščánková, Veronika ; Latta,, Peter (referee) ; Starčuk, Zenon (advisor)
This thesis deals with MR imaging of fluorine-19. Its aim is to prepare phantoms and biological samples for testing of detection sensitivity 19F, to optimize methods of imaging 19F with a preclinical MR system Bruker Biospec 94/30, to examine practical possibilities of imaging 19F on prepared samples and to compare the sensitivity with proton images. Finally, it is necessary to evaluate the results and potential benefits of method.
|
|
|
Contrast enhancement for tissue discrimination and contrast nanoparticle detection by MRI
Bačovský, Jaromír ; Macíček, Ondřej (referee) ; Starčuk, Zenon (advisor)
Magnetic resonance imaging is a routine and powerful diagnostic technique capable of providing detailed information about the structure and composition of the tissues. This diploma thesis is concerned with the mechanisms of contrast origin and contrast modifications by molecular and nanoparticle contrast agents. First sections of the thesis summarize basic knowledge about pulse sequences and it aims to provide an overview on MRI contrast agent with a special emphasis on paramagnetic gadolinium contrast agents and superparamagnetic nanoparticles. The main purpose of this study is to develop the software called MRICalc, which is able to optimize contrast in MRI images. Based on analysis of signal formula of typical pulse sequences, MRICalc is able to propose the parameters of the pulse sequence for compartment-specific enhancement of the contrast. User chooses from the list of the samples and after calculation he obtains the values of echo time, repetition time and flip angle, all of which simultaneously seem to create the appropriate setting to enhance the contrast. MRICalc also allows to plot contrast function with respect to the chosen parameter. Software, including its graphical user interface, is designed in Python. The sample consists from solution of CuSO4 and distilled water was designed to verify the correct function of MRICalc. Sulphate represents a contrast agent. Preclinical MR system Bruker BioSpec 94/30 USR located at Institute of Scientific Instruments of the ASCR, v.v.i was used to measure contrast curve of FLASH pulse sequence, which is a typical representative of gradient echo. Results of the measurement were compared to the theoretical model provided by MRICalc.
|
|
|
Susceptibility weighted magnetic resonance imaging (SWI)
Bačovský, Jaromír ; Bartušek, Karel (referee) ; Starčuk, Zenon (advisor)
Susceptibility weighted magnetic resonance imaging (SWI) seems to be a very promising method usable in the diagnosis of a number of clinical and biomedical applications. Difusse axonal injuries and neurodegenerative diseases to name a few. The goal of my bachelor's thesis was to study the principal methods of magnetic resonance imaging with particular emphasis on susceptibility weighted imaging. Then use this theoretical knowledge for practical implementation of the SWI method to 4,7T/200mm NMR system located at Institute of Scientific Instruments of the ASCR, v.v.i. It was necessary to create an image calculated software, which is capable of enhancing contrast caused by magnetic susceptibility differences as they manifest themselves in local phase changes between tissues. Few basic problems had to be solved. The phase image was filtered by a high pass filter, a Phase Mask was created from adjusted image, which is generated from phase unwrapped image. To varify the SWI method, samples were designed, which have the desired magnetic properties. During the initial phase of experimenting, hen's eggs were used and then citrus fruits with nanoiron, CaCl2, Zn and AgCl. We investigated basic parametres and settings of the MRI measurements that affect final susceptibility weighted image.
|
|
|
SMV-2015-37: Development of an animal model of septic encephalopathy for MR studies, execution and evaluation of a pilot study
Starčuk jr., Zenon
Two animal models of septic encephalopathy in mice were tested: the induction by lipopolysaccharide, and the fecal model, whose objective was to test their applicability in the study of pathophysiology of septic encephalopathy by magnetic resonance in 9.4 Tesla field. Three MR imaging protocols were optimized: T2-weighted RARE for morphological imaging, protocols for native perfusion imaging ASL, and for contrast-enhanced perfusion imaging DCE applying Magnevist, whose main target was the detection of potential changes in the cerebral blood flow and alteration of the blood brain barrier function. Measurements were performed in Bruker Biospec 94/30 with a set of 27 mice anesthesized by isoflurane, whose physiological functions were continuously monitored. The original and analyzed data were provided to the client.
|
|
|
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.
|
guest ::
