Thèses sur le sujet « High resolution 7T MRI »

Temporal lobe epilepsy (TLE) is the most common form of focal epilepsy with 60-75% of cases reported in surgical series. The hippocampus is involved in the genesis of the seizures and hippocampal sclerosis (HS) is the most frequent neuropathological finding observed in surgical samples. However extra-hippocampal neocortical structures may also be involved and the focal cortical dysplasia (FCD) is the most common second alteration frequently associated with HS. Aim of this project was to clarify, both at radiological and neuropathological level, the abnormalities frequently observed in the temporal pole of many TLE patients as the focal cortical dysplasia, the hippocampal sclerosis and the radiological alteration of grey/white matter boundary called “blurring”. The study was performed on surgical specimens of human temporal cortices and hippocampi from TLE patients and autoptic hippocampi at different stage of development submitted first to high resolution (7T) MRI and then processed for histological analysis. Comparison between 7T MRI data with corresponding histological and immunohistochemical features was done. The first part of this study demonstrates that thanks to differences in MRI signal intensities, depending on different density and distribution of cells and myelin fibres, high-resolution ex-vivo MRI enables to visualize the intracortical organization in normal and pathological areas and can detect the subtle architectural alterations in samples presenting dysplastic cortex. The temporo-polar blurring has demonstrated to be due to a great degeneration of fibre bundles in the white matter and, since the age at epilepsy onset is earlier in patients with blurring in comparison to those without blurring, these data suggest that it consists in a slowly evolving chronic degeneration process with the redistribution of the remaining fibres. The comparative imaging-histology investigation on healthy hippocampal specimens shows that 7T MRI can identify the main anatomical structures and the sublayers of the normal hippocampus along its anterior-posterior axis. In sclerotic surgical hippocampi high resolution MRI reveals areas of anomalous hyperintensity of signal associated to marked loss of neurons and intense gliosis as visualized by histological analysis for neuronal and glial cells. Moreover the investigation of intrahippocampal projections performed using fractional anisotropy and fiber tracking, demonstrates a disorganization of fibers in sclerotic samples in comparison to normal hippocampi. The same experimental protocol applied to healthy autoptic hippocampi at different stage of development reveals that during fetal period the MRI signal is related to the cellular density, in fact the regions characterized by densely packed neurons are easily recognizable on ex vivo high field MRI as hypointense areas, while in post-natal specimens the MRI signal is still linked to the cell density but, with the appearance and the progressive increase of the myelin fibers content, this correlation becomes less obvious and the myelin represent the histological component which mainly contributes on MRI signal intensity. This study shows the potential utility of ex-vivo high-field MRI in the understanding of temporal cortical and hippocampal abnormalities, included developmental hippocampal changes, and suggests its possible application in vivo in the near future for the study of several disorders.

Research in lab-on-a-chip (LOC) technology involving microfluidics is a growing field aiming at the development of miniaturized biomedical systems with rich functionality. In order to design effective LOC microfluidic systems, the flow fields and the fluids inside LOC devices need to be carefully characterized. High-resolution magnetic resonance imaging (MRI) offers a powerful non-intrusive technology for this application. In this thesis, the design and implementation of a prototype for a desktop high-resolution MRI instrument, consisting of a magnet, gradient coils, gradient amplifiers, and radio frequency (RF) electronics, is presented. To reduce the size and cost of this MRI instrument, a permanent magnetic configuration with a magnetic flux density of 0.6 T is designed with off-the-shelf NdFeB permanent magnets. The coils of the triaxial gradient module are developed using a novel lithography technique. This gradient module is capable of generating gradient fields as high as 2.83 T/m with custom made current amplifiers. The radio frequency (RF) probe is integrated with the gradient module and is connected to the RF electronics which are made using off-the-shelf components. Pulse sequences and signal processing for acquiring static images and velocity profiles are described. The performance of this instrument in terms of static and dynamic image resolution are presented. As a preliminary test, the velocity profile of water flowing inside a small tube was measured with a nominal resolution of 40 μm. The instrument is designed for a static resolution of better than 30 μm and a velocity resolution better than 50 μm/s. Improvements to the current instrument in addition to theoretical limitations are also detailed.

Equine fetlock region disease is responsible for significant morbidity and mortality. Diagnosis of sesamoidean ligament, cartilage and subchondral bone injury has been obtained by clinical MRI. Low-field MRI provides images helpful in the investigation of MCPJ/MTPJ region pathology in horses in the clinical setting but the greater resolution of high and ultra-field MR images has the potential to aid interpretation through a better understanding of MRI anatomy. Quantitative MRI could provide a non-invasive technique to determine tissue biochemical properties associated with the early onset of articular cartilage degenerative conditions such as osteoarthritis. So far, ultra-high field MRI has not been used in equine research and practice. However, recently 3T MRI has been introduced in equine hospitals in Europe and the US. The general objectives of this project, which utilised cadaver limbs, was to improve understanding of the MRI anatomy of the equine MCPJ/MTPJ region and to evaluate the use of MRI for the non-invasive, quantitative assessment of articular cartilage from the same region. The first specific objective was to describe the appearance of the normal anatomy of the equine MCPJ/MTPJ region, especially the SDFT & DDFT and DSLs, using high field (1.5T) and ultra high field (7T) MRI and to compare the images obtained with the two systems. The second objective was to determine the accuracy and precision of articular cartilage thickness measurements using 1.5T and 7T MRI and comparing the measurements with those made from histological sections of the MCPJ/MTPJ. The third objective was to measure T1 & T2 MRI sequence relaxation times for normal horse articular cartilage pre and post gadolinium contrast (dGEMRIC) administration and to determine their correlation with GAG concentration, including a description of topographical variation. The fourth objective was to compare sodium concentration in normal equine MCPJ/MTPJ articular cartilage measured using 7T MR imaging with a dual tuned quadrature 23Na/1H coil with the biochemical properties (sodium concentration determined by flame photometry and GAG concentration). The final objective was to evaluate MR sodium imaging for the assessment of enzymatically degraded equine cartilage. The findings demonstrated that 7T MRI produces high resolution images, which enable better evaluation of the hard and soft tissues of the equine MCPJ/MTPJ region than images from lower field MR systems and which permit accurate and precise articular cartilage thickness measurements to be made. Moreover, it was found that the dGEMRIC technique appears to provide a feasible quantitative tool for evaluating the articular cartilage properties. However, the quantitative parameters determined by the dGEMRIC method cannot fully characterise the biochemical properties of the cartilage. Moreover, delayed gadolinium-enhanced (dGEMRIC) techniques are time consuming, requiring relatively long incubation and scanning times. The measurement of T2 time is a very complex method. The work described in the last chapters demonstrated that sodium MRI was significantly correlated with the biochemical properties of the equine articular cartilage. Therefore the sodium MRI technique showed promise in imaging articular cartilage and providing useful information on the biochemical properties of the cartilage.

Dosimetry is a vital component of treatment planning in radiation therapy. Methods of radiation dosimetry currently include the use of: ionization chambers, thermoluminescent dosimeters (TLDs), solid-state detectors and radiographic film. However, these methods are inherently either 1D or 2D and their use involves the perturbation of the radiation beam. Although the dose distribution within tissues following radiation therapy treatments can be modeled using computerized treatment planning systems, a need exists for a dosimeter that can accurately measure dose distributions directly and produce 3D dose maps. Some radiation therapy and brachytherapy treatments require mapping the dose distributions in high-resolution (typically < 1 mm). A dosimetry technique that is capable of producing high resolution 3D dose maps of the absorbed dose distribution within tissues is required. Gel dosimetry is inherently a 3D integrating dosimeter that offers high spatial resolution, precision and accuracy. Polymer gel dosimetry is founded on the basis that monomers dissolved in the gel matrix polymerize due to the presence of free radicals produced by the radiolysis of water molecules. The amount of polymerization that occurs within a polymer gel dosimeter can be correlated to the absorbed dose. The gel matrix maintains the spatial integrity of the polymers and hence a dose distribution can be determined by imaging the irradiated polymer gel dosimeter using an imaging modality such as MRI, x-ray computed tomography (CT), ultrasound, optical CT or vibrational spectroscopy. Polymer gel dosimeters, however, suffer from oxygen contamination. Oxygen inhibits the polymerization reaction and hence polymer gel dosimeters must be manufactured, irradiated and scanned in hypoxic environments. Normoxic polymer gel dosimeters incorporate an anti-oxidant into the formulation that binds the oxygen present in the gel and allows the dosimeter to be made under normal atmospheric conditions. The first part of this study was to provide a comprehensive investigation into various formulations of polymer and normoxic polymer gel dosimeters. Several parameters were used to characterize and assess the performance of each formulation of polymer gel dosimeter including: spatial resolution and stability, temporal stability of the R2-dose response, optimal R2-dose response for changes in concentration of constituents and the effects of oxygen infiltration. This work enabled optimal formulations to be determined that would provide greater dose sensitivity. Further work was done to investigate the chemical kinetics that take place within normoxic polymer gel dosimeters from manufacture to post-irradiation. This study explored the functions that each of the constituent chemicals plays in a polymer gel dosimeter. Although normoxic polymer gel dosimeters exhibit very similar characteristics to polyacrylamide polymer gel dosimeters, one important difference between them was found to be a decrease in R2-dose sensitivity over time in the normoxic polymer gel dosimeter compared to an increase in the polyacrylamide polymer gel dosimeters. From an investigation into the function of anti-oxidants in normoxic polymer gel dosimeters, alternatives were proposed. Several alternative anti-oxidants were explored in this study that found that whilst some were reasonably effective, tetrakis (hydroxymethyl) phosphonium chloride (THPC) had the highest reaction rate. THPC was found not only to be an aggressive scavenger of oxygen, but also to increase the dose sensitivity of the gel. Hence, a formulation of normoxic polymer gel dosimeter was proposed, called MAGAT, that comprised: methacrylic acid, gelatin, hydroquinone and THPC. This formulation was examined in a similar fashion to the studies of the other formulations of polymer and normoxic polymer gel dosiemeters. The gel was found to exhibit spatial and temporal stability and an optimal formulation was proposed based on the R2-dose response. Applications such as IVBT require high-resolution dosimetry. Combined with high-resolution MRI, polymer gel dosimetry has potential as a high-resolution 3D integrated dosimeter. Thus, the second component of this study was to commission a micro-imaging MR spectrometer for use with normoxic polymer gel dosimeters and investigate artifacts related to imaging in high-resolutions. Using high-resolution MRI requires high gradient strengths that, combined with the Brownian motion of water molecules, was found to produce an attenuation of the MR signal and hence lead to a variation in the measured R2. The variation in measured R2 was found to be dependent on both the timing and amplitude of pulses in the pulse sequence used during scanning. Software was designed and coded that could accurately determine the amount of variation in measured R2 based on the pulse sequence applied to a phantom. Using this software, it is possible to correct for differences between scans using different imaging parameters or pulse sequences. A normoxic polymer gel dosimeter was irradiated using typical brachytherapy delivery and the resulting dose distributions compared with dose points predicted by the computerized treatment planning system.The R2-dose response was determined and used to convert the R2 maps of the phantoms to dose maps. The phantoms and calibration vials were imaged with an in-plane resolution of 0.1055 mm/pixel and a slice thickness of 2 mm. With such a relatively large slice thickness compared to the in-plane resolution, partial volume effects were significant, especially in the region immediately adjacent the source where high dose gradients typically exist. Estimates of the partial volume effects at various distances within the phantom were determined using a mathematical model based on dose points from the treatment planning system. The normalized and adjusted dose profiles showed very good agreement with the dose points predicted by the treatment planning system.

Dosimetry is a vital component of treatment planning in radiation therapy. Methods of radiation dosimetry currently include the use of: ionization chambers, thermoluminescent dosimeters (TLDs), solid-state detectors and radiographic film. However, these methods are inherently either 1D or 2D and their use involves the perturbation of the radiation beam. Although the dose distribution within tissues following radiation therapy treatments can be modeled using computerized treatment planning systems, a need exists for a dosimeter that can accurately measure dose distributions directly and produce 3D dose maps. Some radiation therapy and brachytherapy treatments require mapping the dose distributions in high-resolution (typically < 1 mm). A dosimetry technique that is capable of producing high resolution 3D dose maps of the absorbed dose distribution within tissues is required. Gel dosimetry is inherently a 3D integrating dosimeter that offers high spatial resolution, precision and accuracy. Polymer gel dosimetry is founded on the basis that monomers dissolved in the gel matrix polymerize due to the presence of free radicals produced by the radiolysis of water molecules. The amount of polymerization that occurs within a polymer gel dosimeter can be correlated to the absorbed dose. The gel matrix maintains the spatial integrity of the polymers and hence a dose distribution can be determined by imaging the irradiated polymer gel dosimeter using an imaging modality such as MRI, x-ray computed tomography (CT), ultrasound, optical CT or vibrational spectroscopy. Polymer gel dosimeters, however, suffer from oxygen contamination. Oxygen inhibits the polymerization reaction and hence polymer gel dosimeters must be manufactured, irradiated and scanned in hypoxic environments. Normoxic polymer gel dosimeters incorporate an anti-oxidant into the formulation that binds the oxygen present in the gel and allows the dosimeter to be made under normal atmospheric conditions. The first part of this study was to provide a comprehensive investigation into various formulations of polymer and normoxic polymer gel dosimeters. Several parameters were used to characterize and assess the performance of each formulation of polymer gel dosimeter including: spatial resolution and stability, temporal stability of the R2-dose response, optimal R2-dose response for changes in concentration of constituents and the effects of oxygen infiltration. This work enabled optimal formulations to be determined that would provide greater dose sensitivity. Further work was done to investigate the chemical kinetics that take place within normoxic polymer gel dosimeters from manufacture to post-irradiation. This study explored the functions that each of the constituent chemicals plays in a polymer gel dosimeter. Although normoxic polymer gel dosimeters exhibit very similar characteristics to polyacrylamide polymer gel dosimeters, one important difference between them was found to be a decrease in R2-dose sensitivity over time in the normoxic polymer gel dosimeter compared to an increase in the polyacrylamide polymer gel dosimeters. From an investigation into the function of anti-oxidants in normoxic polymer gel dosimeters, alternatives were proposed. Several alternative anti-oxidants were explored in this study that found that whilst some were reasonably effective, tetrakis (hydroxymethyl) phosphonium chloride (THPC) had the highest reaction rate. THPC was found not only to be an aggressive scavenger of oxygen, but also to increase the dose sensitivity of the gel. Hence, a formulation of normoxic polymer gel dosimeter was proposed, called MAGAT, that comprised: methacrylic acid, gelatin, hydroquinone and THPC. This formulation was examined in a similar fashion to the studies of the other formulations of polymer and normoxic polymer gel dosiemeters. The gel was found to exhibit spatial and temporal stability and an optimal formulation was proposed based on the R2-dose response. Applications such as IVBT require high-resolution dosimetry. Combined with high-resolution MRI, polymer gel dosimetry has potential as a high-resolution 3D integrated dosimeter. Thus, the second component of this study was to commission a micro-imaging MR spectrometer for use with normoxic polymer gel dosimeters and investigate artifacts related to imaging in high-resolutions. Using high-resolution MRI requires high gradient strengths that, combined with the Brownian motion of water molecules, was found to produce an attenuation of the MR signal and hence lead to a variation in the measured R2. The variation in measured R2 was found to be dependent on both the timing and amplitude of pulses in the pulse sequence used during scanning. Software was designed and coded that could accurately determine the amount of variation in measured R2 based on the pulse sequence applied to a phantom. Using this software, it is possible to correct for differences between scans using different imaging parameters or pulse sequences. A normoxic polymer gel dosimeter was irradiated using typical brachytherapy delivery and the resulting dose distributions compared with dose points predicted by the computerized treatment planning system.The R2-dose response was determined and used to convert the R2 maps of the phantoms to dose maps. The phantoms and calibration vials were imaged with an in-plane resolution of 0.1055 mm/pixel and a slice thickness of 2 mm. With such a relatively large slice thickness compared to the in-plane resolution, partial volume effects were significant, especially in the region immediately adjacent the source where high dose gradients typically exist. Estimates of the partial volume effects at various distances within the phantom were determined using a mathematical model based on dose points from the treatment planning system. The normalized and adjusted dose profiles showed very good agreement with the dose points predicted by the treatment planning system.

La résolution actuelle des IRM pondérées en diffusion suggère qu'il y a entre un et deux tiers des voxels de la matière blanche qui contiennent plusieurs faisceaux de fibres qui se croisent. L'IRM par tenseur de diffusion (DTI) classique est intrinsèquement limitée à ces endroits par son hypothèse de base qu'un seul faisceau traverse chaque voxel de l'image. Le but de cette thèse est donc de développer des techniques d'IRM à haute résolution angulaire (HARDI) pour pouvoir retrouver une ou plusieurs fibres et surmonter aux limites DTI. L'imagerie par q-ball (QBI) est une technique récente qui permet d'estimer la distribution d'orientation des fibres (ODF). La technique de QBI ainsi que l'ODF de diffusion des fibres permettent de retrouver plusieurs directions de fibres en chaque voxel de l'image. Ceux-ci joueront donc un rôle important tout au long de ce document. Cette thèse propose plusieurs contributions originales. D'abord, nous développons l'estimation robuste du signal HARDI en utilisant une base modifiée d'harmoniques sphériques et un terme de régularisation. Ensuite, nous proposons la modélisation du coefficient de diffusion apparent (ADC) pour étudier les mesures d'anisotropie HARDI et faire la classification des voxels contenant une distribution isotrope, une distribution d'une seule population de fibres et une distribution de plusieurs faisceaux fibres. Nous proposons de plus, le développement d'une solution analytique pour estimer l'ODF de diffusion en QBI ainsi qu'un nouvel algorithme de segmentation de ces images d'ODF obtenues par le QBI. Nous présentons également le calcul de l'ODF de fibres avec une nouvelle méthode de déconvolution sphérique à partir des données QBI. Enfin, nous développons de nouveaux algorithmes de suivi de fibres (tracking) déterministes et probabilistes à partir de l'ODF du q-ball et l'ODF de fibres. Finalement, tous ces nouveaux algorithmes sont testés et appliqués sur des données HARDI simulées, sur un fantôme biologique et sur des données réelles de plusieurs sujets dans des régions complexes avec plusieurs faisceaux qui se croisent. Nos résultats illustrent clairement la valeur ajoutée de nos méthodes HARDI sur la plupart des méthodes courantes en DTI qui négligent ces faisceaux complexes, ce qui peut amener à une mauvaise analyse et interprétation de l'anatomie et des fonctions cérébrales
At the current resolution of diffusion-weighted (DW) magnetic resonance imaging (MRI), research groups agree that there are between one third to two thirds of imaging voxels in the human brain white matter that contain fiber crossing bundles. This thesis tackles the important problem of recovering fiber crossing bundles from DW-MRI measurements. The main goal is to overcome the limitations of diffusion tensor imaging (DTI). It is well-known that imaging voxels where there are multiple fiber crossings produce a non-Gaussian DW signal. This is precisely where DTI is limited due to the intrinsic Gaussian assumption of the technique. Hence, this thesis is dedicated to the development of local reconstruction methods, segmentation and tractography algorithms able to infer multiple fiber crossing from DW-MRI data. To do so, high angular resolution diffusion imaging (HARDI) is used to measure DW images along several directions. Q-ball imaging (QBI) is a recent such HARDI technique that reconstructs the diffusion orientation distribution function (ODF), a spherical function that has its maxima aligned with the underlying fiber directions at every voxel. QBI and the diffusion ODF will play a central role in this thesis. There are many original contributions in this thesis. First, we propose a robust estimation of the HARDI signal using a closed-form regularization algorithm based on the spherical harmonics. Then, we estimate the apparent coefficient coefficient (ADC) to study HARDI anisotropy measures and to discriminate voxels with underlying isotropic, single fiber and multiple fiber distributions. Next, we develop a linear, robust and analytical QBI solution using the spherical harmonic basis, which is used in a new statistical region-based active contour algorithm to segment important white matter fiber bundles. In addition, we develop a new spherical deconvolution sharpening method that transforms the diffusion q-ball ODF into a fiber ODF. Finally, we propose a new deterministic tractography algorithm and a new probabilistic tractography algorithm exploiting the full distribution of the fiber ODF. Overall, we show local reconstruction, segmentation and tracking results on complex fiber regions with known fiber crossing on simulated HARDI data, on a biological phantom and on multiple human brain datasets. Most current DTI based methods neglect these complex fibers, which might lead to wrong interpretations of the brain anatomy and functioning

The simultaneous integration of positron emission tomography (PET) and magnetic resonance imaging (MRI) promises to combine superior functional and anatomical information into a single examination, but poses a number of engineering challenges. In particular, the development of MRI-compatible photodetectors is a key issue to realize PET/MRI at its best. In 2009, a novel photodetector, the so-called digital SiPM, was presented. The digital SiPM combines an array of Geiger-mode photodiodes with a direct digital readout and timestamper on a single silicon die. Its high integration and expected immunity to magnetic fields makes the digital SiPM very promising for simultaneous PET/MRI. Related to the development of the world’s first digital SiPM based simultaneous PET/MRI system, this thesis focuses on three specific engineering aspects of simultaneous PET/MRI. First, an MRI-compatible photodetector stack based on digital SiPMs has been developed, investigated and optimized. The final design is virtually immune to the MRI environment and enables the full potential of the digital SiPM to be used for simultaneous PET/MRI, including its time-of-flight capabilities. No evidence was found that the digital SiPM itself is affected by the MRI environment. Second, based on carbon fibre composites, a novel modular radio frequency (RF) shielding concept for MRI-compatible PET detectors has been developed. In contrast to common copper based shields, carbon fibre composites are less susceptible to eddy currents because of their lower sheet conductance. It is shown, experimentally and analytically, that carbon fibre composites can provide higher RF shielding efficiency to sheet conductance ratios than conventional copper shields can do, which makes them beneficial for simultaneous PET/MRI. Third, experimental and simulation approaches for the optical design of pixelated scintillation detectors have been assessed, in particular to improve the depth-of-interaction encoding of pixelated scintillation detectors. A novel pixelated scintillator configuration is proposed, which avoids the use of inter-crystal reflectors.

Magnetic resonance imaging (MRI) is an imaging technique to visualize internal structures of the body. Diffusion MRI is an MRI modality that measures overall diffusion effect of molecules in vivo and non-invasively. Diffusion tensor imaging (DTI) is an extended technique of diffusion MRI. The major application of DTI is to measure the location, orientation and anisotropy of fiber tracts in white matter. It enables non-invasive investigation of major neural pathways of human brain, namely tractography. As spatial resolution of MRI is limited, it is possible that there are multiple fiber bundles within the same voxel. However, diffusion tensor model is only capable of resolving a single direction. The goal of this dissertation is to investigate complex anatomical structures using high angular resolution diffusion imaging (HARDI) data without any assumption on the parameters. The dissertation starts with a study of the noise distribution of truncated MRI data. The noise is often not an issue in diffusion tensor model. However, in HARDI studies, with many more gradient directions being scanned, the number of repetitions of each gradient direction is often small to restrict total acquisition time, making signal-to-noise ratio (SNR) lower. Fitting complex diffusion models to data with reduced SNR is a major interest of this study. We focus on fitting diffusion models to data using maximum likelihood estimation (MLE) method, in which the noise distribution is used to maximize the likelihood. In addition to the parameters being estimated, we use likelihood values for model selection when multiple models are fit to the same data. The advantage of carrying out model selection after fitting the models is that both the quality of data and the quality of fitting results are taken into account. When it comes to tractography, we extend streamline method by using covariance of the estimated parameters to generate probabilistic tracts according to the uncertainty of local tract orientations.

Computed Tomography (CT) is often used for building 3D biomechanical models of human anatomy. This method exposes the subject to a significant x-ray dose and provides limited soft-tissue contrast. Magnetic Resonance Imaging (MRI) is a potential alternative to CT for this application, as MRI offers significantly better soft-tissue contrast and does not expose the subject to ionizing radiation. However, MRI requires long scan times to achieve 3D images at sufficient resolution, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR). These long scan times can make subject motion a problem. This thesis describes my work to reduce scan time while achieving sufficient resolution, SNR, and CNR for 3D biomechanical modeling of (1) the human larynx, and (2) the human hip. I focused on two important strategies for reducing scan time and improving SNR and CNR: the design of RF coils optimized to detect MRI signals from the anatomy of interest, and the determination of MRI relaxation properties of the tissues being imaged (allowing optimization of imaging parameters to improve CNR between tissues). Work on the larynx was done in collaboration with the Thomson group in Mechanical Engineering at BYU. To produce a high-resolution 3D image of the larynx, a 2-channel phased array was constructed. Eight different coil element designs were analyzed for use in the array, and one chosen that provided the highest Q-ratio while still meeting the mechanical constraints of the problem. The phased array was tested by imaging a pig larynx, a good substitute for the human larynx. Excellent image quality was achieved and MR relaxometry was then performed on tissues in the larynx. The work on the hip was done in collaboration with the Anderson group in orthopedics at the University of Utah, who are building models of femoral acetabular impingement (FAI). Accurate imaging of hip cartilage requires injection of fluid into the hip joint capsule while in traction. To optimize contrast, MR relaxometry measurements were performed on saline, isovue, and lidocaine solutions (all typically injected into the hip). Our analysis showed that these substances actually should not be used for MR imaging of the hip, and alternate strategies should be explored as a result.

Current thinking suggests that specialised modules process visual information in a hierarchical manner, using local circuitry in order to maximise efficiency both in terms of wiring costs and stimulus coverage (Reichl et al. (2012)). The resulting organisation has been shown to contain structure in the form of stripes, columns and pinwheels, which in animal models have been linked to functional segregation and specificity. In human cortex, post-mortem investigations have assisted in the visualisation of two such key features: ocular dominance columns (ODC) within V1, and a stripe system within V2 (Adams et al. (2007); Hockfield et al. (1990)). However, functional observations in humans have until recently been beyond the investigatory scope of in-vivo methodology, and as such, a role of these networks has yet to be conclusively determined. In the small number of instances of in-vivo investigations of human ODC and V2 stripes (Cheng et al. (2001); Yacoub et al. (2001); Nasr et al. (2016)), data have been acquired for a small number of carefully selected participants over long scan durations. I aimed to overcome these limitations and explore the functional similarities further, employing a novel, ultra-high resolution fMRI sequence to do so. I measured the cortical response to monocular stimulation and recorded a robust response within V1. However, the regular and repeating functional patterns of ODCs were not observed. Using multivariate techniques I concluded, based on robust classification, that reliable monocular signals were present but that they were subtle and difficult to differentiate from noise. I then investigated the segregation of colour, form and motion within V2, where I found evidence for spatially segregated signals in response to colour and motion, but not to form. I hypothesised that the form stimulus was sub-optimal in driving the neural population of the associated stripes. Based on a limited number of samples, activity in response to colour and motion stimulation conformed on average to the neuroanatomical profile of the V2 stripe system. I suggest that my results offer encouragement for in-vivo investigations of small-scale functional organisation in visual cortex.

A novel MRI method, DIFRAD-FSE (D̲i̲f̲fusion with R̲adial A̲cquisition of D̲ata with F̲ast S̲pin-E̲cho) is presented that enables rapid, high-resolution, multi-shot diffusion-weighted MRI without significant artifacts due to motion. Following a diffusion-weighted spin-echo preparation, multiple radial lines of Fourier data are acquired using spin-echo refocusing. Data can be acquired in either 2D or 3D Fourier space. Motion correction is accomplished via one of four correction techniques: phase correction, shift correction, a combination of the phase and shift correction, or magnitude. Images from a radial data set are reconstructed with filtered back projection reconstruction. Results from human brain imaging will demonstrate the ability of DIFRAD-FSE to acquire high-resolution images without significant artifacts due to motion in both 2D and 3D. Results from liver and heart imaging demonstrate the versatility of the 2D DIFRAD-FSE.

This thesis presents technical and methodological developments aiming tooffer a viable alternative for the treatment of digestive cancers (rectum and esophagus). Compared to the standard methods of therapy, the high intensity contact ultrasound guided by MRI is a less invasive approach. MRI offers 2 advantages: good spatial resolution, and real-time temperature control. This treatment method requires efficacy and safety. Three prototypes of RF coil integrated with ultrasound transducers were built in order to increase the spatial and temporal resolution ofthe MR images, and the accuracy of the temperature measurement. The integrated coils showed a better sensitivity compared to a standard extracorporeal coil. Anatomical (voxel 0.4x0.4x5 mm3)and thermometry (voxel 0.75x0.75x8 mm3, 2s/image) high resolution MR images were acquired in-vivo. The temperature was measured, within a radius of 20 mm from the balloon, with a standard deviation <1°C. The flow artifacts caused by the water circulating inside the cooling balloon could be shifted out of the region of interest. The temperature evolution was controlled automatically, at different depths, with one control point per beam. The controller showed a good accuracy during in-vivo experiments (standard deviation less than 5%). The phased-arrayultra sound transducer permits the successive activation of multiple beams during the same dynamic of sonication. Simulations were conducted in order to offer an optimal treatment planning for a defined tumor. A new design of ultrasound transducer with 256 elements with revolution symmetry, based on a natural geometrical focalization, was proposed.

A number of chronic disease and behavioural factors are recognised to increase the risk of cardiovascular and cerebrovascular diseases. These putative ???vascular??? risk factors have increasingly been recognised to increase the risk of cognitive impairment in the absence of clinically manifest ischemic events. Their relationship to structural brain changes has received limited attention. In this dissertation, I used high resolution magnetic resonance image (MRI) to examine two structural features of the brain, regional gray matter (GM) volumes and silent lacunar infarcts, and determined their association with vascular risk factors. I related these to cognitive function in both cross-sectional and longitudinal studies. The work was based on the data of three waves in two healthy cohorts drawn from the PATH Through Life Study, which is a population-based longitudinal study of ageing comprising 3 cohorts aged 20-24, 40-44, and 60-64 years, with about 2500 participants in each cohort. Random subsamples of Wave 1 of the cohort aged 60-64 years (N = 478) and Wave 2 of the 40+ cohort (aged 44-48 years) (N = 411) were examined cross-sectionally for the MRI sub-study. The MRI cohort aged 60-64 years was re-examined 4 years later in Wave 2. These studies showed that vascular risk factors are associated with lower regional GM volumes and this association varies at different ages. In adults aged 44-48 years, individual risk factors did not show a significant relationship with GM volumes, but the Framingham risk score was associated with less GM volumes in a number of brain regions, suggesting an additive effect of the risk factors. In the 60+ cohort, hypertension was independently associated with less regional GM volumes in bilateral medial frontal, right superior frontal, left superior temporal and precentral gyri. The same cohort, when examined in Wave 2, showed the negative association of hypertension with gray matter volumes to be more widespread. These associations were observed in men but not in women in either wave. Sex dimorphism was observed in the younger cohort as well, with greater GM volumes in temporal and occipital cortices, midbrain and cerebellum in men, while less GM volumes in cingulate and parietal cortices in comparison with women. Lacunar infarcts were present in 7.8 % of the 60+ cohort, and asymptomatic new lacunar lesions developed in 0.4 % per year in this group. The prevalence of lacunar infarcts was correlated with hypertension and a steeper decline in mental speed. These series of studies indicate the relationship of vascular risk factors with changes in brain structure and cognitive function in healthy middle-aged adults. It is suggested that modifying these vascular risk factors may protect the brain from silent lesions and cognitive impairment, and that intervention should begin early in life to have a major impact.

The role of enthesitis in the pathogenesis of psoriatic arthritis has been increasingly recognised in the last twenty years. High resolution imaging techniques and histology have shown that the distal interphalangeal (DIP) joint extensor tendon is directly anchored to the nail. More recently, it has become apparent that a significant proportion of asymptomatic psoriasis patients have subclinical enthesitis at sites such as the Achilles tendon. This thesis explored the hypothesis that nail disease without clinical arthritis was associated with DIP joint enthesopathy and that nail disease equated with remote systemic enthesopathy. Imaging studies utilising magnetic resonance imaging (MRI) of the DIP joint confirmed the relationship between enthesitis and nail disease in psoriatic arthritis, and found subtle enthesitis and osteitis in psoriasis patients. High resolution ultrasound that has an intrinsically greater resolution than MRI showed extensor tendon enthesopathy of the DIP to be common in psoriasis patients with nail disease, but not those without nail disease. It was also shown that nail disease in psoriasis patients without arthritis was associated with sonographically-determined remote enthesopathy in the lower limbs. In a small pilot study (N=9), despite clinical improvements MRI showed ongoing inflammation in and around the DIP joint after six months treatment with a TNF inhibitor. The long term outlook of DIP joint psoriatic arthritis was studied, with a review of a cohort of patients at a mean of nine years after a baseline MRI scan. This demonstrated joint space narrowing in the majority of patients. The development of arthritis mutilans or ankylosis was seen in a minority, but without a close correlation with baseline MRI findings. Collectively these findings show a link between nail disease in psoriasis patients and both local and systemic subclinical enthesopathy.

Thesis (Ph. D.)--Ohio State University, 2004.
Title from first page of PDF file. Document formatted into pages; contains xiv, 222 p. : ill. (some col.). Advisor: Pierre-Marie Luc Robitaille, Dept. of Emergency Medicine. Includes bibliographical references.

L'imagerie par résonance magnétique (IRM) est la technique d'imagerie médicale de référence pour sonder in vivo et non invasivement les tissus mous du corps humain, en particulier le cerveau.L'amélioration de la résolution de l'IRM en un temps d'acquisition standard (400µm isotrope en 15 minutes) permettrait aux médecins d'améliorer considérablement leur diagnostic et le suivi des patients. Cependant, le temps d'acquisition en IRM reste long. Pour réduire ce temps, la récente théorie de l'échantillonnage comprimée (EC) a révolutionné la façon d'acquérir des données dans plusieurs domaines dont l'IRM en surmontant le théorème de Shannon-Nyquist. Avec l'EC, les données peuvent alors être massivement sous-échantillonnées tout en assurant des conditions optimales de reconstruction des images.Dans ce contexte, les thèses de doctorat précédemment soutenue au sein du laboratoire ont été consacrées à la conception et à la mise en oeuvre de scénarios d'acquisition physiquement plausibles pour accélérer l'acquisitions. Un nouvel algorithme d'optimisation pour la conception de trajectoire non cartésienne avancée appelée SPARKLING pour Spreading Projection Algorithm for Rapid K-space samplING en est né. Les trajectoires SPARKLING générées ont conduit à des facteurs d'accélération allant jusqu'à 20 en 2D et 70 pour les acquisitions 3D sur des images à haute résolution pondérées en T*₂ acquises à 7 Tesla. Ces accélérations n'étaient accessibles que grâce au rapport signal/bruit d'entrée élevé fourni par l'utilisation de bobines de réception multi-canaux (IRMp). Cependant, ces résultats ont été obtenus au détriment d'une reconstruction longue et complexe. Dans cette thèse, l'objectif est de proposer une nouvelle approche de reconstruction en ligne d'images acquies par IRMp non cartésiennes. Pour atteindre cet objectif, nous nous appuyons sur une approche en ligne où reconstruction et acquisition s'entremèlent. Par conséquent, la reconstruction débute avant la fin de l'acquisition et un résultat partiel est délivré au cours de l'examen. L'ensemble du pipeline est compatible avec une implémentation réelle à travers l'interface Gadgetron pour produire les images reconstruites à la console du scanner.Ainsi, après avoir exposé la théorie de l'échantillonage comprimé, nous présentons l'état de l'art de la méthode dédiée à la reconstruction en imagerie multi-canaux. En particulier, nous nous concentrerons d'abord sur les méthodes d'autocalibration qui présentent l'avantage d'être adaptées à l'échantillonnage non cartésien et nous proposons une méthode simple mais efficace pour estimer le profil de sensibilité des différents cannaux. Cependant, en raison de leur dépendance au profil de sensibilité, ces méthodes ne sont pas adapatable à la reconstruction en ligne. Par conséquent, la deuxième partie se concentre sur la suppression des ces profils et celà grâce à l'utilisation de norme mixte promouvant une parcimonie structurée. Ensuite, nous adaptons différentes réularization basées sur la parcimonie structurée pour reconstruire ces images fortement corrélées. Enfin, la méthode retenue sera appliquée à l'imagerie en ligne
Magnetic resonance imaging (MRI) is the reference medical imaging technique for probing in vivo and non-invasively soft tissues in the human body, notably the brain. MR image resolution improvement in a standard scanning time (e.g., 400µm isotropic in 15 min) would allow medical doctors to significantly improve both their diagnosis and patients' follow-up. However the scanning time in MRI remains long, especially in the high resolution context. To reduce this time, the recent Compressed Sensing (CS) theory has revolutionized the way of acquiring data in several fields including MRI by overcoming the Shannon-Nyquist theorem. Using CS, data can then be massively under-sampled while ensuring conditions for optimal image recovery.In this context, previous Ph.D. thesis in the laboratory were dedicated to the design and implementation of physically plausible acquisition scenarios to accelerate the scan. Those projects deliver new optimization algorithm for the design of advanced non-Cartesian trajectory called SPARKLING: Spreading Projection Algorithm for Rapid K-space samplING. The generated SPARKLING trajectories led to acceleration factors up to 20 in 2D and 60 for 3D-acquisitions on highly resolved T₂* weighted images acquired at 7~Tesla.Those accelerations were only accessible thanks to the high input Signal-to-Noise Ratio delivered by the usage of multi-channel reception coils. However, those results are coming at a price of long and complex reconstruction.In this thesis, the objective is to propose an online approach for non-Cartesian multi-channel MR image reconstruction. To achieve this goal we rely on an online approach where the reconstruction starts from incomplete data.Hence acquisition and reconstruction are interleaved, and partial feedback is given during the scan. After exposing the Compressed Sensing theory, we present state-of the art method dedicated to multi-channel coil reconstruction. In particular, we will first focus on self-calibrating methods that presents the advantage to be adapted to non-Cartesian sampling and we propose a simple yet efficient method to estimate the coil sensitivity profile.However, owing to its dependence to user-defined parameters, this two-step approach (extraction of sensitivity maps and then image reconstruction) is not compatible with the timing constraints associated with online reconstruction. Then we studied the case of calibration-less reconstruction methods and splits them into two categories, the k-space based and the domain-based. While the k-space calibration-less method are sub-optimal for non-Cartesian reconstruction, due to the gridding procedure, we will retain the domain-based calibration-less reconstruction and prove theirs for online purposes. Hence in the second part, we first prove the advantage of mixed norm to improve the recovery guarantee in the pMRI setting. Then we studied the impact of structured sparse induced norm on the reconstruction multi-channel purposes, where then and adapt different penalty based on structured sparsity to handle those highly correlated images. Finally, the retained method will be applied to online purposes. The entire pipeline, is compatible with an implementation through the Gadgetron pipeline to deliver the reconstruction at the scanner console

The recurrent laryngeal nerve (RLN) innervates all the intrinsic muscles of the larynx that are responsible for human vocalization and language. The RLN runs along the tracheoesophageal groove bilaterally and is often accidentally damaged or transected during head and neck surgical procedures. RLN palsy and vocal cord paralysis are the most common and serious post op complications of thyroid surgeries. Patients who suffer from RLN injury can develop unilateral or bilateral vocal fold paralysis (BVFP). Theoretically, selective reinnervation of the posterior cricoarytenoid muscle would be the best treatment for BVFP. The phrenic nerve has been shown in several studies to be the best candidate to anastomose to the distal end of a severed RLN to restore glottal abduction. Successful PCA reinnervation has been sporadically achieved in both human patients and in animal models. Another notable ramification of recurrent laryngeal nerve injury is vocal instability caused by the alteration of mechanical properties within the larynx. In phonosurgery, alterations to the position and framework of the laryngeal apparatus are made to improve voice quality. Accurate and realistic synthetic models are greatly needed to predict the outcome of various adjustments to vocal cord tension and position that could be made surgically. Despite the sporadically successful attempts at PCA reinnervation, thus far, there are still several deficits in our anatomical familiarity and technological capability, which hinder the regularity of successful PCA reinnervation surgeries and our capacity to generate synthetic models of the human larynx that are both realistic and functional. We will address three of these deficits in this project using the porcine larynx as a model. Firstly, we will identify the anatomical variations of the porcine recurrent laryngeal nerve branches. A microscribe digitizer will be used to create three-dimensional mapping of the recurrent laryngeal nerve branches that are relevant to the posterior cricoarytenoid muscle and the abduction of the vocal folds. Secondly, we will develop a magnetic resonance imaging technique to correlate recurrent laryngeal nerve branching patterns with high-resolution MR images that can be used to determine the branching patterns present in a given specimen without surgery. Lastly, we will determine the distribution and composition of different tissue types found within human vocal folds. High resolution MRI, and Mallory's trichrome and H&E histological staining will be used to distinguish and identify the tissue composition of the vocal folds and surrounding laryngeal structures. Detailed information regarding vocal fold tissue composition and histological geometry will enable laryngeal modelers to select more sophisticated and life-like materials with which to construct synthetic vocal fold models.

This thesis concerns the cortical connectivity in Primates. The efficacy of Diffusion weighted MRI (dMRI) is examined. White matter (“WM”) systems subjacent to cortex (“superficial WM” ) are found to be a limiting factor to dMRI tractography. Superficial WM systems are examined with dMRI itself, and with analysis of histological data from the scanned brains. dMRI data was acquired ex-vivo at exceptional spatial and angular resolution (250μm in Rhesus, 150μm in Marmoset). The superficial WM was found to be complex, and with current dMRI methods, an effective barrier to tracking to and from around 50% of cortex in Rhesus. The quality of our data allowed Gray matter seeding, so that penetration both into and out of cortex was examined. We summarize the history of cortical connectivity and current work in tractography. We present an account of the formation and properties of the superficial WM. We compare tracking behaviors to tracer results, and develop a series of scalar maps on cortical surface models to summarize tracking behaviors. We attempt to explain these maps by examining the underlying tracking behavior and the brain tissue itself, revealing the intricate nature of the superficial WM. Chapter 4 contains a separate but related project in which a histologically accurate high resolution 3D and surface atlas of the Rhesus cortex is constructed with unprecedented accuracy. A method to rapidly and accurately non-linearly transform the atlas to a scan of another animal is developed, thus labelling its cortex. accuracy is by comparison to histology of the scanned animals.

The present work is concerned with the development of a non-invasive method of examining the detailed structure of the human cerebral cortex using high resolution structural magnetic resonance imaging (MRI). The relationship between MR images of the brain and the cortical features giving rise to them was investigated in a post mortem study of human striate cortex.

L’imagerie par résonance magnétique (IRM) est un outil d’investigation majeur donnant accès de manière non invasive à des nombreuses informations quantitatives et fonctionnelles. La qualité des images obtenues (rapport-signal-sur-bruit, RSB) est cependant limitée dans certaines applications nécessitant des résolutions spatiales et/ou temporelles poussées. Afin d’améliorer la sensibilité de détection des équipements d’IRM, diverses orientations peuvent être suivies telles qu’augmenter l’intensité du champ magnétique des imageurs, améliorer les performances des systèmes de détection radiofréquence (RF), ou encore développer des séquences d’acquisition et des techniques de reconstruction d’images plus efficaces. La thématique globale dans laquelle s’inscrit cette thèse concerne le développement des systèmes de détection RF à haute sensibilité pour l’IRM à haut champ chez l’homme. En particulier, des antennes auto-résonantes basées sur le principe des lignes de transmission sont utilisées parce qu’elles peuvent être réalisée sur substrat souple. Cette adaptabilité géométrique du résonateur permet d’ajuster précisément sa forme aux spécificités morphologiques de la zone anatomique observée, et ainsi d’augmenter le RSB. La première visée technologique de ce projet concerne le développement, de la conception jusqu’à la mise en œuvre dans un appareil 7 T corps entier, d’un système de détection RF flexible à haute sensibilité, utilisant des antennes miniatures associées en réseau. L’utilisation d’un réseau d’antennes miniatures permet d’obtenir des images sur un champ de vue élargi tout en conservant la haute sensibilité inhérente à chaque antenne miniature. De plus, la technologie de l’imagerie parallèle devient accessible, ce qui permet d’accélérer l’acquisition des images. De surcroît, un nouveau schéma de résonateur de ligne transmission avec un degré de liberté supplémentaire est introduit, ce qui permet de réaliser de grands résonateurs multi-tours pour l’IRM à haut champ. Cette thèse décrit le développement, la mise en œuvre et l’évaluation des nouveaux systèmes de détection RF au moyen de simulations analytiques et numériques, et des études expérimentales
Magnetic resonance imaging (MRI), among other imaging techniques, has become a major backbone of modern medical diagnostics. MRI enables the non-invasive combined, identification of anatomical structures, functional and chemical properties, especially in soft tissues. Nonetheless, applications requiring very high spatial and/or temporal resolution are often limited by the available signal-to-noise ratio (SNR) in MR experiments. Since first clinical applications, image quality in MRI has been constantly improved by applying one or several of the following strategies: increasing the static magnetic field strength, improvement of the radiofrequency (RF) detection system, development of specialized acquisition sequences and optimization of image reconstruction techniques. This work is concerned with the development of highly sensitive RF detection systems for biomedical ultra-high field MRI. In particular, auto-resonant RF coils based on transmission line technology are investigated. These resonators may be fabricated on flexible substrate which enables form-fitting of the RF detector to the target anatomy, leading to a significant SNR gain. The main objective of this work is the development of a flexible RF coil array for high-resolution MRI on a human whole-body 7 T MR scanner. With coil arrays, the intrinsically high SNR of small surface coils may be exploited for an extended field of view. Further, parallel imaging techniques are accessible with RF array technology, allowing acceleration of the image acquisition. Secondly, in this PhD project a novel design for transmission line resonators is developed, that brings an additional degree of freedom in geometric design and enables the fabrication of large multi-turn resonators for high field MR applications. This thesis describes the development, successful implementation and evaluation of novel, mechanically flexible RF devices by analytical and 3D electromagnetic simulations, in bench measurements and in MRI experiments

Diffusion-weighted magnetic resonance imaging (MRI) has allowed unprecedented non-invasive mapping of brain neural connectivity in vivo by means of fiber tractography applications. Fiber tractography has emerged as a useful tool for mapping brain white matter connectivity prior to surgery or in an intraoperative setting. The advent of high angular resolution diffusion-weighted imaging (HARDI) techniques in MRI for fiber tractography has allowed mapping of fiber tracts in areas of complex white matter fiber crossings. Raw HARDI images, as a result of elevated diffusion-weighting, suffer from depressed signal-to-noise ratio (SNR) levels. The accuracy of fiber tractography is dependent on the performance of the various methods extracting dominant fiber orientations from the HARDI-measured noisy diffusivity profiles. These methods will be sensitive to and directly affected by the noise. In the first part of the thesis this issue is addressed by applying an objective and adaptive smoothing to the noisy HARDI data via generalized cross-validation (GCV) by means of the smoothing splines on the sphere method for estimating the smooth diffusivity profiles in three dimensional diffusion space. Subsequently, fiber orientation distribution functions (ODFs) that reveal dominant fiber orientations in fiber crossings are then reconstructed from the smoothed diffusivity profiles using the Funk-Radon transform. Previous ODF smoothing techniques have been subjective and non-adaptive to data SNR. The GCV-smoothed ODFs from our method are accurate and are smoothed without external intervention facilitating more precise fiber tractography. Diffusion-weighted MRI studies in amyotrophic lateral sclerosis (ALS) have revealed significant changes in diffusion parameters in ALS patient brains. With the need for early detection of possibly discrete upper motor neuron (UMN) degeneration signs in patients with early ALS, a HARDI study is applied in order to investigate diffusion-sensitive changes reflected in the diffusion tensor imaging (DTI) measures axial and radial diffusivity as well as the more commonly used measures fractional anisotropy (FA) and mean diffusivity (MD). The hypothesis is that there would be added utility in considering axial and radial diffusivities which directly reflect changes in the diffusion tensors in addition to FA and MD to aid in revealing neurodegenerative changes in ALS. In addition, applying adaptive smoothing via GCV to the HARDI data further facilitates the application of fiber tractography by automatically eliminating spurious noisy peaks in reconstructed ODFs that would mislead fiber tracking.

En microscopie IRM, la sensibilité de détection est critique pour obtenir des images avec un rapport signal sur bruit suffisant car l’intensité du signal RMN devient extrêmement faible. Une stratégie alternative à l’utilisation de champs statiques élevés consiste à améliorer les performances des antennes radiofréquences qui détectent le signal d’IRM. Plus particulièrement, la stratégie dans laquelle s’inscrit ce travail de thèse vise à exploiter la haute sensibilité des antennes miniatures supraconductrices basées sur le principe des résonateurs monolithiques à ligne de transmission avec comme objectif à terme la mise en réseau de ce type d’antennes. Le développement d’un tel réseau représente un enjeu instrumental majeur car cela permet de profiter de la haute sensibilité intrinsèque des antennes miniatures supraconductrices tout en autorisant l’observation de zones étendues ou en profondeur. Cependant, les caractéristiques géométriques de ces antennes et la nature des matériaux utilisés posent des difficultés importantes pour réaliser les opérations d’accord, d’adaptation, ou découplage mutuel lors de leur utilisation en IRM. Dans le cadre de cette thèse, nous avons conduit des travaux abordant ces différentes problématiques et permettant la mise œuvre d’un réseau supraconducteur pour l’imagerie haute résolution à champ clinique.Nous avons développé en premier lieu un système permettant de réaliser automatiquement et sans contact l’accord et l’adaptation des antennes miniatures monolithiques. Ce système utilise des techniques, basées sur le couplage électrique et magnétique, que nous avons préalablement étudiées en utilisant différentes méthodes. Les performances de ce système ont été étudiées et la faisabilité de sa mise en œuvre dans une expérience d’IRM a été établie.Nous avons abordé en second lieu le problème de découplage mutuel des éléments constituant un réseau. Pour cela, des techniques de découplage potentiellement compatibles avec les antennes miniatures supraconductrices ont été étudiées. En particulier, la technique de découplage par anneau de blindage a été investie en profondeur, par simulation numérique et expérimentalement, et nous avons développé un modèle analytique d’optimisation du niveau de découplage accessible par cette technique. Nous avons mis en œuvre et validé cette technique avec des réseaux en cuivre de quatre antennes et des premiers essais ont été conduits avec un réseau constitué de deux antennes miniatures supraconductrices
In MRI microscopy, the sensitivity of the detection is a critical issue for acquiring images with high signal to noise ratio because the amount of NMR signal is extremely low. An alternative to the use of high field strength is to improve the performances of the radiofrequency coil that detect the NRM signal. In particular, the strategy underlying the present work aims at exploiting the high sensitivity of miniature superconducting coils based on the monolithic design of transmission line resonators, with the long term objective of implementing an array of these coils. The development of such array represents an important instrumental stake since it allows for benefiting from the intrinsically high sensitivity of miniature superconducting coils while allowing the observation of extended region of interest. However, the highly compact structure, the small size of the coil and the nature of the material used make rise important difficulties for achieving the tuning, matching and mutual decoupling when using these coils in MRI. In the frame of this PhD project, with conducted works to address these problematics and allow for implementing a superconducting array for high resolution imaging at clinical filed strength.We have firstly developed a control system which allows for automatic and contactless tuning and matching of miniature monolithic coils. This system uses techniques based on electric and magnetic coupling, that we beforehand investigated using various methods. The performances of this system were studied and the feasibility of implementing it in an MRI experiment was established.The second part of this work addresses the issue of mutual decoupling between the elements of an array elements. To this end, decoupling techniques being potentially compatible with miniature superconducting coils have been studied. In particular the decoupling technique using shielding rings has been deeply investigated, by numerical simulation and experimentally, and we have developed an analytical model for optimizing the decoupling level achievable with this technic. We have implemented and validated this technic with a four-element copper coil array and first trials were performed with an array of two miniature.superconducting coils

La structure et l'organisation de la substance blanche du cerveau humain ne sont pas encore complètement connues. L'Imagerie par Résonance Magnétique de diffusion (IRMd) offre une approche unique pour étudier in vivo la structure des tissus cérébraux, permettant la reconstruction non invasive des trajectoires des faisceaux de fibres du cerveau en utilisant la tractographie. Aujourd'hui, les techniques récentes d'IRMd avec haute résolution angulaire (HARDI) ont largement amélioré la qualité de la tractographie par rapport à l'imagerie du tenseur de diffusion standard (DTI). Toutefois, les jeux de données de tractographie résultant sont très complexes et comprennent des millions de fibres, ce qui nécessite une nouvelle génération de méthodes d'analyse. Au-delà de la cartographie des principales voies de la substance blanche, cette nouvelle technologie ouvre la voie à l'étude des faisceaux d'association courts, qui ont rarement été étudiés avant et qui sont au centre de cette thèse. L'objectif est d'inférer un atlas des faisceaux de fibres du cerveau humain et une méthode qui permet le mappage de cet atlas à tout nouveau cerveau.Afin de surmonter la limitation induite par la taille et la complexité des jeux de données de tractographie, nous proposons une stratégie à deux niveaux, qui enchaîne des regroupements de fibres intra- et inter-sujet. Le premier niveau, un regroupement intra-sujet, est composé par plusieurs étapes qui effectuent un regroupement hiérarchique et robuste des fibres issues de la tractographie, pouvant traiter des jeux de données contenant des millions de fibres. Le résultat final est un ensemble de quelques milliers de faisceaux de fibres homogènes représentant la structure du jeu de données de tractographie dans sa totalité. Cette représentation simplifiée de la substance blanche peut être utilisée par plusieurs études sur la structure des faisceaux individuels ou des analyses de groupe. La robustesse et le coût de l'extensibilité de la méthode sont vérifiés à l'aide de jeux de fibres simulés. Le deuxième niveau, un regroupement inter-sujet, rassemble les faisceaux obtenus dans le premier niveau pour une population de sujets et effectue un regroupement après normalisation spatiale. Il produit en sortie un modèle composé d'une liste de faisceaux de fibres génériques qui peuvent être détectés dans la plupart de la population. Une validation avec des jeux de données simulées est appliqué afin d'étudier le comportement du regroupement inter-sujet sur une population de sujets alignés avec une transformation affine. La méthode a été appliquée aux jeux de fibres calculés à partir des données HARDI de douze cerveaux adultes. Un nouveau atlas des faisceaux HARDI multi-sujet, qui représente la variabilité de la forme et la position des faisceaux à travers les sujets, a été ainsi inféré. L'atlas comprend 36 faisceaux de la substance blanche profonde, dont certains représentent quelques subdivisions des faisceaux connus, et 94 faisceaux d'association courts de la substance blanche superficielle. Enfin, nous proposons une méthode de segmentation automatique de mappage de cet atlas à tout nouveau sujet.

Magnetic resonance imaging (MRI) is the preferred imaging modality for visualization of intracranial soft tissues. Surgical planning, and increasingly surgical navigation, use high resolution 3-D patient-specific structural maps of the brain. However, the process of MRI is a multi-parameter tomographic technique where high resolution imagery competes against high contrast and reasonable acquisition times. Resolution enhancement techniques based on super-resolution are particularly well suited in solving the problems of resolution when high contrast with reasonable times for MRI acquisitions are needed. Super-resolution is the concept of reconstructing a high resolution image from a set of low-resolution images taken at dierent viewpoints or foci. The MRI encoding techniques that produce high resolution imagery are often sub-optimal for the desired contrast needed for visualization of some structures in the brain. A novel super-resolution reconstruction framework for MRI is proposed in this thesis. Its purpose is to produce images of both high resolution and high contrast desirable for image-guided minimally invasive brain surgery. The input data are multiple 2-D multi-slice Inversion Recovery MRI scans acquired at orientations with regular angular spacing rotated around a common axis. Inspired by the computed tomography domain, the reconstruction is a 3-D volume of isotropic high resolution, where the inversion process resembles a projection reconstruction problem. Iterative algorithms for reconstruction are based on the projection onto convex sets formalism. Results demonstrate resolution enhancement in simulated phantom studies, and in ex- and in-vivo human brain scans, carried out on clinical scanners. In addition, a novel motion correction method is applied to volume registration using an iterative technique in which super-resolution reconstruction is estimated in a given iteration following motion correction in the preceding iteration. A comparison study of our method with previously published methods in super-resolution shows favorable characteristics of the proposed approach.

Involviert in Netzwerke für das episodische Gedächtnis sowie als Bestandteil des Hypothalamus und des limbischen Systems stellen sich die im Zwischenhirn gelegenen Mamillarkörper als Zielstruktur im Kontext affektiver Störungen dar. Bislang waren die Mamillarkörper diesbezüglich lediglich in einer postmortem durchgeführten Studie Gegenstand der Forschung; es liegen keine Untersuchungen mit Hilfe der 7 Tesla-Magnetresonanztomografie vor. Um diese neuen Möglichkeiten der in vivo-Volumetrie im Submillimeterbereich auszuschöpfen, wurde auf Grundlage einer farbkodierten Darstellung ein detaillierter Algorithmus entwickelt, der sich als Hauptergebnis der vorliegenden Arbeit als hoch reliabel erwies. In der vorliegenden Pilotstudie wurde darüber hinaus das Mamillarkörper-Volumen von 14 Patientinnen und Patienten mit einer Bipolaren Störung und 20 gesunden Kontrollpersonen anhand von hochaufgelösten T1-gewichteten MRT-Bildern bestimmt. Ein signifikanter Unterschied zwischen den beiden Gruppen konnte nicht nachgewiesen werden, ebenso kein Unterschied zwischen den Geschlechtern. Es konnte gezeigt werden, dass das Volumen der Mamillarkörper signifikant invers mit dem Alter der ProbandInnen korreliert. Des Weiteren wurde eine signifikante positive Korrelation mit dem Gesamthirnvolumen der ProbandInnen festgestellt. Krankheitsschwere und Episodenzahl hingegen hatten keinen Einfluss auf das Mamillarkörper-Volumen. Die Ergebnisse dieser Pilotstudie sollten anhand einer größeren Stichprobe überprüft werden.

Diffusion-weighted (DW) magnetic resonance imaging is an important neuroimaging technique that has successful applications in diagnosis of ischemic stroke and methods based on diffusion tensor imaging (DTI). Tensor measures have been used for detecting changes in tissue microstructure and for non-invasively tracing white matter connections in vivo. The most common image acquistion strategy is to use a DW single-shot echo-planar imaging (ss-EPI) pulse sequence, which is attractive due to its robustness to motion artefacts and high imaging speed. However, this sequence has limited achievable spatial resolution and suffers from geometric distortion and blurring artefacts. Readout-segmented echo-planar imaging (rs-EPI) is a DW sequence that is capable of acquiring high-resolution images by segmenting the acquisition of k- space into multiple shots. The fast, short readouts reduce distortion and blurring and the problem of artefacts due to motion-induced phase changes between shots can be overcome with navigator techniques. The rs-EPI sequence has two main shortcomings. (i) The method is slow to produce image volumes, which is limiting for clinical scans due to patient welfare and prevents us from acquiring very many directions in DTI. (ii) The sequence (like other diffusion techniques) is far from the optimum repetition time (TR) for acquiring data with the highest possible signal-to-noise ratio (SNR) in a given time. The work in this thesis seeks to address both of these important issues using a range of approaches. In Chapter 4 a partial Fourier extension is presented, which addresses point (i) by reducing the number of readout segments acquired and estimating the missing data. This allows reductions in scan time by approximately 40% and the reliability of the images is demonstrated in comparisons with the original images. The application of a simultaneous multi-slice scheme to rs-EPI, to address points (i) and (ii), is described in Chapter 5. Using the slice-accelerated rs-EPI sequence, tractography data were compared to ss-EPI data and high-resolution trace-weighted data were acquired in clinically relevant scan times. Finally, a 3D multi-slab extension that addresses point (i) is presented in Chapter 6. A 3D sequence could also allow higher resolution in the slice direction than 2D multi-slice methods, which are limited by the difficulties in exciting thin, accurate slices. A 3D version of rs-EPI was simulated and implemented and a k-space acquisition synchronised to the cardiac cycle showed substantial improvements in image artefacts compared to a conventional k-space acquisition.

L’utilisation intensive des produits phytosanitaires, en particulier les insecticides, provoque des effets indésirables sur les organismes vivants et leur environnement. Mon travail de thèse a consisté à évaluer l’effet de deux insecticides chez un insecte modèle la drosophile. Une première étude concernait l’effet d’un néonicotinoïde, l’imidaclopride. Nous avons pu montrer que l’exposition chronique à des doses sublétales de cet insecticide perturbe la fonction de reproduction chez la drosophile. D’autre part, une exposition aiguë à l’imidaclopride a mis en évidence une résistance chez les femelles d’une souche de drosophile dite ``des champs´´. Deux mécanismes différents ont été mis en évidence dans la résistance à l’imidaclopride de cette souche. Le premier concerne la sous expression d’une sous-unité (D1) du récepteur nicotinique à l’acétylcholine, cible de l’imidaclopride. Le deuxième concerne l’implication des glutathion S-transférases, enzymes de détoxification, dans le métabolisme de l’imidaclopride. Ces études montrent que les insecticides peuvent avoir en plus des effets sur les insectes ravageurs, des effets néfastes sur des organismes non cibles. La deuxième étude avait pour but de modéliser chez la drosophile, l’impact d’un organochloré, la dieldrine, potentiellement impliquée dans la maladie de Parkinson chez l’homme. L’exposition à cet insecticide conduit à une dégénérescence des neurones dopaminergiques ainsi qu’une perturbation de la structure de régions particulières du cerveau. Nous avons également montré des altérations du métabolisme et l’implication de processus épigénétiques dans la neurodégénérescence induite par la dieldrine. Au cours de ce travail, nous avons pu montrer l’intérêt de nouvelles méthodes comme l’Imagerie par Résonance Magnétique (IRM) ou le High Resolution Magic Angle Spinning (HRMAS) dans ce type d’étude
Pesticides have been used extensively and induce harmful effects on organisms and their environment. The aim of my PhD work was to investigate the effects of two insecticides by using Drosophila as a model. The first study concerns the effect of a neonicotinoid, imidacloprid. The results obtained have shown that a chronic exposure at sublethal doses of this insecticide affects reproduction in flies. Moreover, acute exposure at high doses has pointed out a resistance phenomenon in females of a field strain. We have shown that two mechanisms are implicated: (i) low expression of a subunit of a nicotinic acetylcholine receptor that is the target of imidaclopride and (ii) role of glutathione S-transférases, detoxication enzymes, in imidaclopride metabolism. These results highlight impact of insecticides, in particular imidaclopride, on non target organisms. The aim of the second study was to characterize in Drosophila, effects of an organochlorine, dieldrin, potentially implicated in the etiology of Parkinson’s disease in humans. Dieldrin exposure at low doses promotes neurodegeneration of dopaminergic neurons and alters structures of particular regions of the brain. Disruption of metabolism is also induced after exposition to dieldrin. In addition, we have shown that epigenetic processes are implicated in neurodegenration induced by dieldrin. This work show advantages of new techniques such as Magnetic Resonance Imaging (MRI) and High Reslution Magic Angle Spinning in this kind of study

L'imagerie de diffusion (IRMd) est une méthode unique permettant d'étudier la microstructure cérébrale et la connectivité du cerveau de manière non-invasive. Cependant, la faible résolution et la qualité de cette imagerie restreint son utilisation dans certaines applications. L'objectif de cette thèse est de développer l'IRMd cérébrale à très haute résolution sur un modèle de macaque anesthésié au moyen d'une séquence d'imagerie 3D écho-planaire segmentée (3D-msEPI) à 3T. Après une étape de développement de la reconstruction et du post-traitement des données, nous avons réalisé des images de diffusion sur le cerveau de macaque à une résolution spatiale isotrope de 0.5mm. Cette résolution nous a permis de délimiter et caractériser les structures fines comme les sous-couches de l'hippocampe ou la matière blanche superficielle, qui sont indétectables avec des séquences classiques. Cependant, cette méthode se révèle vulnérable aux mouvements élastiques des tissus cérébraux induits par les pulsations cardio-vasculaires. Une stratégie de synchronisation de l'acquisition sur celle-ci nous a permis de caractériser leurs effets sur l'IRMd à très haute résolution chez le singe anesthésié. Ces effets se caractérisent par des artefacts de ghosting et des pertes de signal qui corrompent les images, le tenseur et la tractographie dans des zones spécifiques du cerveau. La synchronisation nous a ainsi permis de réaliser une imagerie de diffusion cérébrale de macaque à des résolutions spatiales et des pondérations en diffusion très élevées jamais atteintes auparavant. Ces résultats préliminaires démontrent le potentiel de notre méthode pour les applications neuroscientifiques et médicales chez l'homme
Diffusion imaging (dMRI) is a unique method for studying brain microstructure and brain connectivity in a non-invasive way. However, the low resolution and quality of this imaging restricts its use in some applications. The aim of this thesis is to develop very high resolution cerebral MRI on an anesthetized macaque model on a 3T scanner using a segmented 3D echo-planar 3D imaging sequence (3D-msEPI). After a stage of development of the reconstruction and post-processing of the data, we made diffusion images on the macaque brain at an isotropic spatial resolution of 0.5mm. This resolution allowed us to delineate and characterize fine structures such as hippocampal sublayers or superficial white matter, which are undetectable with classical sequences. However, this method is vulnerable to the elastic movements of the brain tissue induced by the cardiovascular pulsations. A strategy of synchronization of the acquisition on this one allowed us to characterize their effects on the very high resolution MRI in the anesthetized monkey. These effects are characterized by ghosting artifacts and signal losses that corrupt images, tensor, and tractography in specific areas of the brain. The synchronization allowed us to realize macaque brain diffusion imaging at spatial resolutions and very high diffusion weights never reached before. These preliminary results demonstrate the potential of our method for neuroscientific and medical applications in humans

Thesis (Ph.D.)--Worcester Polytechnic Institute.
Keywords: Mn54-autoradiography, rat retina, manganese enchanced mri, rcs rat, magnetic resonance imaging, retinal degeneration, high-resolution mri, blood volume imaging Includes bibliographical references (leaves 211-226).

L’IRM de diffusion (IRMd) est l’unique technique non invasive qui permet l’exploration de la microstructure cérébrale. En plus d’une large utilisation pour les applications médicales, l’IRMd est aussi utilisée en neuroscience pour comprendre l’organisation et le fonctionnement du cerveau. Toutefois, sa faible résolution spatiale et sa sensibilité aux artéfacts limitent son utilisation chez le primate non humain.L’objectif de cette étude est de développer une nouvelle approche qui permette d’acquérir des données d’IRMd à très haute résolution spatiale sur des cerveaux de macaques anesthésiés. Cette méthode est basée sur un balayage 3D de l’espace de Fourier avec un module de lecture d’Echo Planar-segmenté.Cette méthode a été tout d’abord implémentée sur une machine IRM 3 Tesla (Prisma, Siemens), puis validée et optimisée in-vitro et in-vivo. Par rapport à la méthode d’acquisition classique, un gain de sensibilité de l’ordre de 3 pour la substance grise cérébrale et de 4.7 pour la substance blanche cérébrale a été obtenu grâce à la méthode développée.Cette méthode a permis de réaliser l’IRMd du cerveau de Macaque avec une résolution spatiale isotrope de 0.5 mm jamais atteinte auparavant. L’intérêt de réaliser des données d’IRMd à une telle résolution pour visualiser et analyser in-vivo des structures fines non détectables avec la méthode d’acquisition classique comme les sous-champs de l’hippocampe ou encore la substance blanche superficielle, a été démontré dans cette étude. Des résultats préliminaires très encourageants ont également été obtenus chez l’homme
Diffusion MRI (dMRI) is the unique non-invasive technique that allows exploring the cerebral microstructure. Besides a wide use for medical applications, dMRI is also employed in neuroscience to understand the brain organization and connectivity. However, the low spatial resolution and the sensitivity to artefacts limit its application to non-human primates.This work aims to develop a new approach that allows to acquire dMRI at very high spatial resolution on anesthetized macaque brains. This method is based on a 3D sampling of Fourier space with a segmented Echo Planar imaging readout module. This method has been firstly implemented on a 3 Tesla MR scanner (Prisma, Siemens), validated and optimized in-vitro and in-vivo. Compared to the conventional acquisition method, a gain of sensitivity of 3 for the cerebral grey matter and of 4.7 for the white matter was obtained with the proposed approach.This method allowed us to acquire dMRI data on the macaque brain with a spatial isotropic resolution of 0.5 mm ever reached before. The interest to acquire dMRI data with such a spatial resolution to visualize and analyze in-vivo fine structures not detectable with the classical acquisition method, like the sub-fields of hippocampus and the superficial white matter, has also illustrated in this study. Finally, very encouraging preliminary results were also obtained in humans

Mit dieser Arbeit ist es erstmalig gelungen, funktionelle MRT und Dipol-Quellenlokalisation in einer Weise zu kombinieren, die es erlaubt, ein und dieselbe kortikale Aktivität simultan mit beiden Verfahren zu erfassen. Insbesondere wurde dies durch (a) Korrektur eines vom Tomographen induzierten Artefaks in den EKPs und (b) durch eine deutliche Verbesserung des experimentellen Designs, und damit einer wesentlich effektiveren Nutzung von EEG und fMRT-Messzeit erreicht. So wurde es dadurch möglich, mit beiden Methoden die kortikale Aktivität einer Einzelpulsstimulation noch aufzulösen. Eine wesentliche Voraussetzung für die simultane Kombination beider Verfahren: Aufgrund der sehr verschiedenen Latenzen von elektrophysiologischer (< 1ms) und vaskulärer (SII->ant. Inseln und medialeWand) in Übereinstimmung mit der Literatur (Forss et al., 1996; Mauguiere et al., 1997b) blieb. So ergab die Quellenlokalisation für die Wahlreaktionsaufgabe fünf Dipole innerhalb des Gehirns, welche mittels Koregistrierung den Aktivierungen des primären somatosensorschen Kortex (20 - 140ms), des sekundären somatosensorischen Kortex (50 - 150ms), der beiden anterioren Inseln (80 - 140ms) und des supplementär-motorischen Region (90 - 140ms, 220 - 270ms) aus der funktionellen MRT zugeordnet wurden. Durch einen Vergleich der Aktivierungsmuster von Wahl- und Einfachreaktionsaufgabe jeweils in der Dipol-Quellenanalyse und in der funktionellen MRT konnten weitere Belege dafür gefunden werden, daß, wie in der Literatur postuliert (Romo and Salinas, 2001), der kontralaterale sekundäre somatosensorische Kortex an der Kategorisierung somatosensorischer Stimulusattribute beteiligt ist. So ergab ein Vergleich der Dipolzeitverläufe für Wahl- und Einfachreaktionsaufgabe lediglich für den Dipol im kontralateral somatosensorischen Kortex im Intervall 57-62 ms nach Stimulusapplikation einen signifikant unterschiedlichen Aktivierungsverlauf (p < 0,001). Übereinstimmend zeigte die funktionelle MRT für die Wahlreaktionsaufgabe neben einer stärkeren Aktivierung der SMA eine hochsignifikant stärkere Aktivierung im Areal des kontralateralen sekundären somatosensorischen Kortex (p-cluster < 0,001).
In this study, we have shown that it is feasible to perform dipole source analysis and fMRI based on the same neuronal activity associated with somatosensory categorization. This was possible by reduction of scanner-induced baseline artifact interfering with the ERPs as well as an optimized experimental protocol for interleaved EEG and fMRI acquisition. We consider this study to be a further step toward imaging brain activity simultaneously at high spatial and temporal resolution. Since an event-related protocol with a single brief pulse stimulation paradigm was successfully employed, this approach seems to be suitable for the investigation of cognitive tasks. By further technical improvements also the exploration of brain activity in single subjects might become possible, opening the field of clinical applications. In particular for the characterization of irregular and nonreproducible events, a substantial contribution of combined EEG–fMRI studies toward a more detailed understanding of physiological processes underlying cerebral activations is expected.

L'un des problèmes fondamentaux de l'imagerie cardiaque par résonance magnétique du tenseur de diffusion (IRM-TD) est sa faible résolution spatiale, à cause des limitations matérielles des scanners IRM actuels. L'objectif principal de ce travail de thèse est de développer de nouvelles approches pour améliorer la résolution des données d'IRM-TD afin de mieux représenter l'architecture myocardique du coeur humain et de la comparer avec des résultats issus d'autres techniques d'investigation telles que l'imagerie par lumière polarisée. Dans ce cadre, le travail porte sur trois parties principales. La première concerne le développement d'une nouvelle approche pour l'interpolation des champs de vecteurs propres principaux issus de l'IRM-TD cardiaque humaine. Cette approche consiste d'abord à supprimer les vecteurs corrompus par le bruit au lieu de débruiter de manière uniforme le champ entier de vecteurs, et ensuite à interpoler le champ de vecteurs en utilisant la modèle Thin-Plate-Spline (TPS) afin d'exploiter la corrélation entre les composantes du vecteur. La deuxième partie concerne une nouvelle famille de méthodes d'interpolation pour les champs de tenseurs, basée soit sur les angles d'Euler soit sur le quaternion. Ces méthodes exploitent les caractéristiques du tenseur et préservent les paramètres de tenseurs, tels que le déterminant du tenseur, l'anisotropie fractionnelle (FA) et la diffusivité moyenne (MD). En outre, cette partie compare les principales approches d'interpolation au niveau des images pondérées en diffusion et des champs de tenseurs, et les résultats montrent qu'il serait préférable d'effectuer l'interpolation des données d'IRM-TD au niveau des champs de tenseurs. La troisième partie étudie le changement des paramètres MD et FA après un infarctus du myocarde chez les cochons, et l'influence des méthodes d'interpolation sur ces paramètres dans la zone infarctus et la zone distante. Les résultats montrent que la zone infarctus présente une diminution significative de FA et une augmentation significative de MD, comparée avec la zone distante, et que les méthodes d'interpolations du tenseur ont plus d'influence sur FA que sur MD, ce qui suggère que l'interprétation de ces paramètres cliniques après l'interpolation doive être prise avec précaution.

碩士
國立臺灣大學
生醫電子與資訊學研究所
100
Recently, the functional magnetic resonance imaging (fMRI) has become a booming technique in the desire of understanding our mysterious brains. However, the blood oxygen level-dependent (BOLD) signal of the fMRI studies is very weak which could be influenced by noise easily. Therefore, if the noise of the fMRI studies could be reduced, the functional contrast-to-noise ratio (CNR) and the significance of the functional connectivity will considerably increase. In order to improve the accuracy and reliability of the fMRI results, the high-temperature superconducting (HTS) radio-frequency (RF) surface coil platform in 7 Tesla (T) animal Magnetic Resonance Imaging (MRI) system served as a novel implementation for the fMRI studies. In the reason, the thermal noise of the MRI system could be reduced for its extremely low resistance attribute under critical temperature (Tc). The results showed that the rat brain anatomy image SNR gain was about 1.8 times by using HTS RF surface coil platform compared to homemade copper RF surface coil of similar size and shape. In the block-design fMRI experiment of forepaws electrical stimulation, the HTS RF surface coil platform demonstrated a 1.5-time functional CNR gain. Besides, the temporal SNR was also improved by using HTS RF surface coil platform with approximately 1.4 times gain in the resting-state fMRI experiment. Furthermore, the functional connectivity of sensorimotor system, including motor cortex (M1/M2), somatosensory cortex (S1/S2), and thalamus, also became much more significant due to the thermal noise reduction as scanned by HTS RF surface coil platform. As shown in the results of this study, the image SNR, temporal SNR, functional CNR, and the significance of the functional connectivity were all improved greatly as the thermal noise was reduced by using HTS RF surface coil platform. The brain functional connectivity would be revealed more accurately using the HTS RF surface coil platform. In the future, more information and knowledge, including reliable brain network causality analysis, would be feasible by using the high SNR HTS RF surface coil platform.

The noninvasive magnetic resonance imaging technique allows for the investigation of functional processes in the living plant. For this purpose during this work, different NMR imaging methods were further developed and applied. For the localisation of the intrusion of water into the germinating rape seed with the simultaneous depiction of the lipid-rich tissue via a 3D rendering, in Chap. 5 the technique of interleaved chemical selective acquisition of water and lipid was used in the germinating seed. The utilization of high-resolution MR images of germinated seeds enabled the localization of a predetermined water gap in the lipid-rich aleurone layer, which resides directly under the seed coat. The for a long time in biology prevalent discussion, whether such a gap exists or the seed soaks up the water from all sides, rather like a sponge, could hereby, at least for the rapeseed seed, be answered clearly. Furthermore, the segmentation and 3D visualization of the vascular tissue in the rapeseed seeds was enabled by the high-resolution datasets, a multiply branched structure preconstructed in the seed could be shown. The water is directed by the vascular tissue and thus awakens the seed gradually to life. This re-awakening could as well be tracked by means of invasive imaging via an oxygen sensor. In the re-awakened seeds, the lipid degradation starts, other than expected, not in the lipid-rich cotyledons but in the residual endosperm remaining from seed development and in the aleurone layer which previously protected the embryo. Within this layer, the degradation could be verified in the high-resolution MR datasets. The method presented in Chap. 6 provides a further characteristic trait for phenotyping of seeds and lipid containing plants in general. The visualization of the compounds of fatty acids in plant seeds and fruits could be achieved by the distinct utilization of chemical shift-selective imaging techniques. Via the application of a CSI sequence the fatty acid compounds in an olive were localized in a 2D slice. In conjunction with an individually adjusted CHESS presaturation module Haa85 the high-resolution 3D visualization of saturated and unsaturated fatty acid compounds in different seeds was achieved. The ratio maps calculated from these datasets allow to draw conclusions from the developmental stage or the type of seed. Furthermore, it could be shown that the storage condition of two soybean seeds with different storage time durations lead to no degradation of the fatty acid content. Additional structural information from inside of dry seeds are now accessible via MRI. In this work the imaging of cereal seeds could be significantly improved by the application of the UTE sequence. The hitherto existing depictions of the lipid distribution, acquired with the spin echo sequence, were always sufficient for examinations of the lipid content, yet defects in the starchy endosperm or differences in the starch concentration within the seed remained constantly unseen with this technique. In a direct comparison of the datasets acquired with the previous imaging technique (spin echo) and with UTE imaging, the advantage of data acquisition with UTE could be shown. By investigating the potential seed compounds (starch, proteins, sugar) in pure form, the constituent parts contributing to the signal could be identified as bound water (residual moisture) and starch. The application of a bi-exponential fit on the datasets of the barley seed enabled the separate mapping of magnetization and of relaxation time of two components contributing to the NMR signal. The direct comparison with histological stainings verified the previous results, thus this technique can be used for the selective imaging of starch in dry seeds. Conclusions on the translocation characteristics in plants can be drawn by the technique proposed in Chap. 8. The associated translocation velocities can now, even in the range of several um/h, be determined in the living plant. Based on calculated concentrations of an MR contrast agent, which was taken up by the plant, these translocation velocities were estimated both in longitudinal direction, thus along the vascular bundle, and in horizontal direction, thus out of the bundle. The latter velocity is located below the contrast agent's velocity value of free diffusion. By adjusting a dynamic contrast-enhancing imaging technique (DCE-Imaging, Tof91) the acquisition duration of a T1-map was significantly reduced. By means of these maps, local concentrations of the contrast agent in plant stems and the siliques of the rapeseed plant could be determined. Numerous questions in plant science can only be answered by non-invasive techniques such as MRI. For this reason, besides the experimental results achieved in this work, further NMR methods were tested and provided for the investigation of plants. As an example, the study on the imaging of magnetic exchange processes are mentioned, which provided the groundwork for a possible transfer of CEST experiments (Chemical Exchange Saturation Transfer) to the plant. The results are presented in the bachelor thesis of A. Jäger Jae17, which was performed under my supervision, they find great interest under biologists. The development of new technologies, which extend the possibilities for the investigation of living organisms, is of great importance. For this reason, I have contributed to the development of the currently unpublished method RACETE (Refocused Acquisition of Chemical Exchange Transferred Excitations [Jak17, Reu17, Gut18a]). By rephasing the transferred magnetization the utilization of properties which have not been available in chemical "`exchange"' experiments is enabled. With this method a positive contrast is generated, thus a reference experiment is not mandatory. Furthermore, the image phase, which in classical experiments contains no information about the exchanged protons, can be used for the distinct identification of multiple substances which have been excited simultaneously. This recently at the Department of Experimental Physics V developed method can be used in particular for the identification of lipids and for the localization of sugars and amino acids, thus it can serve the enhancement and improvement of non-invasive analytical methods
Die nicht-invasive Bildgebungstechnik der Magnetresonanz ermöglicht es, funktionelle Prozesse in Pflanzen am lebenden Objekt zu untersuchen. Hierfür wurden im Rahmen dieser Arbeit verschiedene NMR-Bildgebungsmethoden weiterentwickelt und angewendet. Da Pflanzen ein magnetisch sehr inhomogenes Gewebe besitzen, bedingt durch Lufteinschlüsse und das Vorhandensein verschiedenster gelöster Stoffe im Pflanzengewebe, wurden daher hauptsächlich Spin-Echo-Methoden für die Bildgebung verwendet. Um das erste Eindringen des Wassers in den keimenden Raps-Samen bei gleichzeitiger Darstellung des lipid-reichen Gewebes mittels einer 3D-Visualisierung zu lokalisieren, wurde in Kapitel 5 die Technik der verschachtelten, chemisch selektiven Aufnahme von Wasser und Lipid im keimenden Samen verwendet. Durch Verwendung von hochausgelösten MR-Aufnahmen an gekeimten Samen konnte weiterhin in der lipid-reichen Aleuron-Schicht, die sich direkt unter der Samenschale befindet, ein gezielt angelegter Einlass für das Wasser verortet werden. Die in der Biologie lange Zeit verbreitete Diskussion, ob es einen solchen Einlass gibt oder der keimende Samen das Wasser eher wie ein Schwamm von allen Seiten aufsaugt, konnte hierdurch, zumindest für den Raps-Samen, eindeutig beantwortet werden. Weiterhin konnte durch die hoch-aufgelösten Aufnahmen das vaskuläre Gewebe in den Raps-Samen segmentiert und in 3D veranschaulicht werden, es zeigte sich eine mehrfach verzweigte Struktur, die bereits im Samen angelegt ist. Das Wasser folgt hierbei dem vaskulären Gewebe und erweckt hierdurch den Samen schrittweise zum Leben. Dieses Wieder-Erwachen konnte ebenfalls durch die invasive Bildgebung mittels eines Sauerstoff-Sensors nachverfolgt werden. Im nun erwachten Samen selbst beginnt der Lipid-Abbau, anders als zunächst angenommen, nicht in den lipid-haltigen Kotyledonen sondern im von der Samen-Entwicklung verbliebenden Endosperm und in der den Keimling vormals schützenden Aleuron-Schicht. In dieser konnte der Abbau an gekeimten Samen durch hochaufgelöste MR-Aufnahmen nachgewiesen werden. Die in Kapitel 6 vorgeschlagene Methode liefert ein weiteres Merkmal zur Phenotypisiserung von Samen und lipidhaltigen Pflanzenbestandteilen im Allgemeinen. Die Darstellung der Bestandteile ungesättigter Fettsäuren in Pflanzensamen und -Früchten konnte durch gezielte Verwendung von chemisch selektiven Bildgebungstechniken erreicht werden. Durch die Anwendung einer CSI-Sequenz konnten die Fettsäurebestandteile in Oliven in einer 2D-Schicht lokalisiert werden. In Verbindung mit einem jeweils angepassten CHESS-Vorsättigungsmodul Haa85 wurde die hochaufgelöste 3D-Darstellung von gesättigten und ungesättigten Fettsäurebestandteilen in unterschiedlichen Samen erreicht. Rückschlüsse über das Entwicklungsstadium sowie die Sorte der verwendeten Samen können aus den Verhältnis-Karten, die aus den jeweiligen Datensätzen berechnet wurden, gezogen werden. Dass in diesem Fall die Aufbewahrungsmethode zu keiner Degradation der Fettsäurezusammensetzung geführt hat, konnte weiterhin am Beispiel von zwei Sojasamen mit unterschiedlicher Lagerdauer gezeigt werden. Zusätzliche strukturelle Informationen aus dem Inneren trockener Samen sind nun mittels MRT zugänglich. In dieser Arbeit konnte durch die UTE-Sequenz die Bildgebung von Getreidesamen deutlich vorangebracht werden. Die bisherigen Darstellungen der Lipid-Verteilung, aufgenommen mit einer Spin-Echo Sequenz, waren zwar für die Betrachtung des Lipid-Gehalts stets ausreichend, Defekte im stärkehaltigen Endosperm oder Unterschiede in der Stärke-Konzentration innerhalb des Samen blieben mit dieser Technik jedoch stets verborgen. Im direkten Vergleich der mit der bisherigen Technik (Spin-Echo) und der UTE-Bildgebung aufgenommenen Datensätze konnte der Vorteil der Datenaufnahme mit UTE gezeigt werden. Durch die Untersuchung der möglichen Samenbestandteile (Stärke, Proteine, Zucker) in Reinform konnten die zum Signal beitragen Bestandteile als gebundenes Wasser (Restfeuchte) und Stärke identifiziert werden. Die Verwendung bi-exponentiellen Fits and die Messdaten ermöglichte es im Gersten-Samen, zwei zum Signal beitragende Komponenten in getrennten Karten bezüglich ihrer Magnetisierung und Relaxationszeit zu trennen. Der Vergleich mit histologischen Färbungen bestätigte die bisherigen Ergebnisse, somit kann diese Technik zur selektiven Darstellung von Stärke in trockenen Samen verwendet werden. Rückschlüsse auf das Transportverhalten in Pflanzen können durch die in Kapitel 8 vorgestellte Technik gezogen werden. Die zugehörigen Transportgeschwindigkeiten im lebenden Pflanzenobjekt können nun, selbst im Bereich von wenigen $\mu$m/h, bestimmt werden. Diese wurden anhand von berechneten Konzentrationen eines von der Pflanze aufgenommenen MR-Kontrastmittels sowohl in longitudinaler Richtung, also entlang des Leitgewebebündels, als auch in horizontaler Richtung, also aus dem Leitbündel heraus, abgeschätzt werden; Letztere Geschwindigkeit liegt deutlich unter dem Wert der freien Diffusionsgeschwindigkeit des Kontrastmittels. Hierfür wurden durch Anpassung einer dynamischen Kontrast-erhöhenden Bildgebungstechnik (DCE-Imaging, Tof91) die Aufnahmedauer einer für die weiteren Berechnungen benötigen T1-Karte deutlich reduziert. Mittels dieser Karten konnten die lokalen Konzentrationen des Kontrastmittels in Pflanzenstängeln und Schoten der Rapspflanze bestimmt werden. Zahlreiche Fragen in der Pflanzenforschung können nur durch nicht-invasive Techniken wie MRT beantwortet werden. Deswegen wurden, neben den experimentellen Ergebnissen, die mittels dieser Arbeit erreicht wurden, auch weitere NMR Methoden für die Untersuchung von Pflanzen getestet und zur Verfügung gestellt. Als Beispiel seien hier die Untersuchungen zur Bildgebung von magnetischen Austauschprozessen genannt, welche eine Vorarbeit zur möglichen Übertragung con CEST-Experimenten (Chemical Exchange Saturation Transfer) auf das Modell Pflanze liefern. Die Ergebnisse sind in der Bachelor-Arbeit von A. Jäger \cite{jaeger17}, an deren Durchführung ich als Betreuer maßgeblich beteiligt war, dargestellt und finden großes Interesse bei Biologen. Von besonderer Wichtigkeit sind auch die Entwicklungen neuer Technologien, die die Möglichkeiten zur Untersuchung von lebenden Organismen erweitern können. Deswegen habe ich zu der Entwicklung der bislang unveröffentlichten Methode RACETE (Refocused Acquisition of Chemical Exchange Transferred Excitations [Jak17, Reu17, Gut18a]) beigetragen. Durch das Rephasieren der transferierten Magnetisierung können Eigenschaften, die bislang in chemischen "`Austausch"'-Experimenten nicht zur Verfügung stehen, ausgenutzt werden. Mit dieser Methode wird ein positiver Kontrast erzeugt, sie ist deshalb nicht zwingend auf ein Referenz-Experiment angewiesen. Weiterhin kann die Bildphase, welche in klassichen CEST-Experimenten keine Information über die ausgetauschten Protonen enthält, zur eindeutigen Identifizierung mehrerer parallel angeregter Substanzen verwendet werden