Coil combination using linear deconvolution in k-space for phase imaging

Background: The combination of multi-channel data is a critical step for the imaging of phase and susceptibility contrast in magnetic resonance imaging (MRI). Magnitude-weighted phase combination methods often produce noise and aliasing artifacts in the magnitude images at accelerated imaging sceneries. To address this issue, an optimal coil combination method through deconvolution in k-space is proposed in this paper. Methods: The proposed method firstly employs the sum-of-squares and phase aligning method to yield a complex reference coil image which is then used to calculate the coil sensitivity and its Fourier transform. Then, the coil k-space combining weights is computed, taking into account the truncated frequency data of coil sensitivity and the acquired k-space data. Finally, combining the coil k-space data with the acquired weights generates the k-space data of proton distribution, with which both phase and magnitude information can be obtained straightforwardly. Both phantom and in vivo imaging experiments were conducted to evaluate the performance of the proposed method. Results: Compared with magnitude-weighted method and MCPC-C, the proposed method can alleviate the phase cancellation in coil combination, resulting in a less wrapped phase. Conclusions: The proposed method provides an effective and efficient approach to combine multiple coil image in parallel MRI reconstruction, and has potential to benefit routine clinical practice in the future

Accelerating Quantitative Susceptibility Mapping using Compressed Sensing and Deep Neural Network

Quantitative susceptibility mapping (QSM) is an MRI phase-based post-processing method that quantifies tissue magnetic susceptibility distributions. However, QSM acquisitions are relatively slow, even with parallel imaging. Incoherent undersampling and compressed sensing reconstruction techniques have been used to accelerate traditional magnitude-based MRI acquisitions; however, most do not recover the full phase signal due to its non-convex nature. In this study, a learning-based Deep Complex Residual Network (DCRNet) is proposed to recover both the magnitude and phase images from incoherently undersampled data, enabling high acceleration of QSM acquisition. Magnitude, phase, and QSM results from DCRNet were compared with two iterative and one deep learning methods on retrospectively undersampled acquisitions from six healthy volunteers, one intracranial hemorrhage and one multiple sclerosis patients, as well as one prospectively undersampled healthy subject using a 7T scanner. Peak signal to noise ratio (PSNR), structural similarity (SSIM) and region-of-interest susceptibility measurements are reported for numerical comparisons. The proposed DCRNet method substantially reduced artifacts and blurring compared to the other methods and resulted in the highest PSNR and SSIM on the magnitude, phase, local field, and susceptibility maps. It led to 4.0% to 8.8% accuracy improvements in deep grey matter susceptibility than some existing methods, when the acquisition was accelerated four times. The proposed DCRNet also dramatically shortened the reconstruction time by nearly 10 thousand times for each scan, from around 80 hours using conventional approaches to only 30 seconds.Comment: 10 figure

A comparison of static and dynamic ∆B0 mapping methods for correction of CEST MRI in the presence of temporal B0 field variations

Purpose: To assess the performance, in the presence of scanner instabilities, of three dynamic correction methods which integrate ∆B 0 mapping into the chemical exchange saturation transfer (CEST) measurement and three established static ∆B 0 -correction approaches. Methods: A homogeneous phantom and five healthy volunteers were scanned with a CEST sequence at 7 T. The in vivo measurements were performed twice: first with unaltered system frequency and again applying frequency shifts during the CEST acquisition. In all cases, retrospective voxel-wise ∆B 0 -correction was performed using one intrinsic and two extrinsic [prescans with dual-echo gradient-echo and water saturation shift referencing (WASSR)] static approaches. These were compared with two intrinsic [using phase data directly generated by single-echo or double-echo GRE (gradient-echo) CEST readout (CEST-GRE-2TE)] and one extrinsic [phase from interleaved dual-echo EPI (echo planar imaging) navigator (NAV-EPI-2TE)] dynamic ∆B 0 -correction approaches [allowing correction of each Z-spectral point before magnetization transfer ratio asymmetry (MTR asym) analysis]. Results: All three dynamic methods successfully mapped the induced drift. The intrinsic approaches were affected by the CEST labeling near water (∆ω < |0.3| ppm). The MTR asym contrast was distorted by the frequency drift in the brain by up to 0.21%/Hz when static ∆B 0 -corrections were applied, whereas the dynamic ∆B 0 corrections reduced this to <0.01%/Hz without the need of external scans. The CEST-GRE-2TE and NAV-EPI-2TE resulted in highly consistent MTR asym values with/without drift for all subjects. Conclusion: Reliable correction of scanner instabilities is essential to establish clinical CEST MRI. The three dynamic approaches presented improved the ∆B 0 -correction performance significantly in the presence of frequency drift compared to established static methods. Among them, the self-corrected CEST-GRE-2TE was the most accurate and straightforward to implement

Otimização de sequências e ferramentas de processamento para quantificação do ferro (QSM)

As doenças neurodegenerativas, como o caso das doenças de Parkinson, Huntington e Tremor Essencial não possuem, atualmente, terapias de cura, mas sim tratamentos que prolongam a vida e melhoram a qualidade de vida dos pacientes. Todavia, têm vindo a ser feitos esforços por parte de investigadores para descobrir os mecanismos da génese destas patologias de modo a tornar possível o seu diagnóstico precoce e com isso estudar estratégias de implementação de novas soluções. Assim, esta dissertação surge no seguimento de uma serie de trabalhos que se focaram particularmente na caracterização destas doenças. Especificamente, este estudo utilizou dados de pacientes do Hospital Santa Maria (Lisboa) submetidos a protocolos de sequências de aquisição de imagens multi-eco de ressonância magnética de 3T em 2D e 3D ponderadas em T2 e T2* para diagnóstico da doença de Parkinson tendo-se concentrado na otimização destes, na otimização de ferramentas e mecanismos para o seu pós-processamento. Focou-se também na quantificação do ferro como um biomarcador relevante nas regiões normalmente afetadas, como é o caso dos núcleos da base (globo pálido, putamen, núcleo caudado, substantia nigra e núcleo rubro). Nestes núcleos ocorre acumulação anómala de ferro ligada à progressão da neurodegeneração, segundo estudos recentes. Nesta tese foi utilizada uma técnica conhecida como mapeamento quantitativo de suscetibilidade magnética (QSM – Quantitative Susceptibility Mapping), que avalia a diferença de suscetibilidades magnéticas entre tecidos, que por sua vez indicam o balanço entre paramagnetismo e diamagnetismo das espécies moleculares presentes. Utilizando software designado para este fim, criado por investigadores de Cornell MRI Research Lab, que se baseia no algoritmo MEDI (Morphology Enabled Dipole Inversion) geraram-se, depois de algumas adaptações ao código original, os mapas das suscetibilidades, cujos volumes de interesse foram em seguida segmentados de forma automática e manual, de modo a se estimarem os valores de suscetibilidade (médias e desvios padrão) das estruturas segmentadas. Compararam-se os resultados obtidos das suscetibilidades entre os vários ecos, as várias estruturas, entre as aquisições 2D e 3D e entre pacientes considerados como controlo e aqueles com sinais de neurodegeneração, tendo sido demonstrada a viabilidade dos parâmetros de aquisição, métodos de processamento e ferramentas de mapeamento e segmentação utilizadas e comprovada a acumulação de ferro nos volumes de interesse, proporcional aos valores de suscetibilidade obtidos

Double volumetric navigators for real-time simultaneous shim and motion measurement and correction in Glycogen Chemical Exchange Saturation Transfer (GlycoCEST) MRI

Glycogen is the primary glucose storage mechanism in in living systems and plays a central role in systemic glucose homeostasis. The study of muscle glycogen concentrations in vivo still largely relies on tissue sampling methods via needle biopsy. However, muscle biopsies are invasive and limit the frequency of measurements and the number of sites that can be assessed. Non-invasive methods for quantifying glycogen in vivo are therefore desirable in order to understand the pathophysiology of common diseases with dysregulated glycogen metabolism such as obesity, insulin resistance, and diabetes, as well as glycogen metabolism in sports physiology. Chemical Exchange Saturation Transfer (CEST) MRI has emerged as a non-invasive contrast enhancement technique that enables detection of molecules, like glycogen, whose concentrations are too low to impact the contrast of standard MR imaging. CEST imaging is performed by selectively saturating hydrogen nuclei of the metabolites that are in chemical exchange with those of water molecules and detecting a reduction in MRI signal in the water pool resulting from continuous chemical exchange. However, CEST signal can easily be compromised by artifacts. Since CEST is based on chemical shift, it is very sensitive to field inhomogeneity which may arise from poor initial shimming, subject respiration, heating of shim iron, mechanical vibrations or subject motion. This is a particular problem for molecules that resonate close to water, such as - OH protons in glycogen, where small variations in chemical shift cause misinterpretation of CEST data. The purpose of this thesis was to optimize the CEST MRI sequence for glycogen detection and implement a real-time simultaneous motion and shim correction and measurement method. First, analytical solution of the Bloch-McConnell equations was used to find optimal continuous wave RF pulse parameters for glycogen detection, and results were validated on a phantom with varying glycogen concentrations and in vivo on human calf muscle. Next, the CEST sequence was modified with double volumetric navigators (DvNavs) to measure pose changes and update field of view and zero- and first-order shim parameters. Finally, the impact of B0 field fluctuations on the scan-rescan reproducibility of CEST was evaluated in vivo in 9 volunteers across 10 different scans. Simulation results showed an optimal RF saturation power of 1.5µT and duration of 1s for glycoCEST. These parameters were validated experimentally in vivo and the ability to detect varying glycogen concentrations was demonstrated in a phantom. Phantom data showed that the DvNav-CEST sequence accurately estimates system frequency and linear shim gradient changes due to motion and corrects resulting image distortions. In addition, DvNav-CEST was shown to yield improved CEST quantification in vivo in the presence of motion and motion-induced field inhomogeneity. B0 field fluctuations were found to lower the reproducibility of CEST measures: the mean coefficient of variation (CoV) for repeated scans was 83.70 ± 70.79 % without shim correction. However, the DvNav-CEST sequence was able to measure and correct B0 variations, reducing the CoV to 2.6 ± 1.37 %. The study confirms the possibility of detecting glycogen using CEST MRI at 3 T and shows the potential of the real-time shim and motion navigated CEST sequence for producing repeatable results in vivo by reducing the effect of B0 field fluctuations

Assessing Midbrain Abnormalities In Parkinson’s Disease Using Magnetic Resonance Imaging

Diagnosing early-stage Parkinson’s disease (PD) and its manifestations is still a clinical challenge. Previous imaging studies using iron, neuromelanin (NM) and the Nigrosome-1 (N1) measures in the substantia nigra (SN) by themselves have been unable to provide sufficiently high diagnostic performance for these methods to be adopted clinically. In this dissertation, we start by studying idiopathic PD patients at their intermediate stages of the disease to evaluate the role of global and regional iron in the major deep gray matter nuclei. Then, we only focus on the NM complex in the midbrain and how neuronal loss interact with iron overload as well as their relationship with clinical scores strictly on early PD patients. Finally, by taking one more step back in the disease progression process, we investigate the impact of iron deposition and N1 appearance in idiopathic rapid eye movement sleep behavior disorder (RBD) as the prodromal stage of PD. The results of this work are summarized as the following: 1) the increase in iron in the SN in some PD patients is higher than the normal range in healthy controls (HC) as found in both regional and global analyses and that regional high iron content may provide a means to separate two populations of PD patients; one with and one without iron increases in the SN; 2) we have introduced a rapid five-minute 3D approach to depict NM degeneration and iron deposition simultaneously which provides a practical MR imaging method to differentiate early stage subjects with PD from HCs with an approximately 98% accuracy; and finally 3) iRBD patients were found to have a higher incidence of N1 loss, reduced volume and elevated iron levels in a few brain structures as well as cognitive and motor impairment scores being correlated with iron deposition of several cerebral nuclei. All these in vivo biomarkers put together can significantly contribute to a better understanding of the underlying pathophysiology in PD onset and progression with the ultimate goal being a more confident clinical diagnosis prior to symptomatic dysfunction

Brain hypothermia in ischemic stroke: non-invasive thermometry and molecular basis

Ischemic stroke is a leading cause of death and morbidity around the world. However, only one pharmacological treatment is currently available, the tissue plasminogen activator or rtPA. Preclinical studies demonstrated the high therapeutic potential of hypothermia to mitigate the effects of stroke, but this therapy has not been successfully translated to the clinics due to the side effects associated to cold (shivering, arrhythmia, or pneumonia among others), and due to the lack of non-invasive methods to assess brain temperature. The present work provides new data about the therapeutic potential of focal brain hypothermia as alternative to systemic cooling, the use of non-invasive magnetic resonance thermometry to measure brain temperature, and the possible implication of RBM3, a cold shock protein, in the molecular process underlying the protective effect of cold

Preclinical MRI of the Kidney

This Open Access volume provides readers with an open access protocol collection and wide-ranging recommendations for preclinical renal MRI used in translational research. The chapters in this book are interdisciplinary in nature and bridge the gaps between physics, physiology, and medicine. They are designed to enhance training in renal MRI sciences and improve the reproducibility of renal imaging research. Chapters provide guidance for exploring, using and developing small animal renal MRI in your laboratory as a unique tool for advanced in vivo phenotyping, diagnostic imaging, and research into potential new therapies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Preclinical MRI of the Kidney: Methods and Protocols is a valuable resource and will be of importance to anyone interested in the preclinical aspect of renal and cardiorenal diseases in the fields of physiology, nephrology, radiology, and cardiology. This publication is based upon work from COST Action PARENCHIMA, supported by European Cooperation in Science and Technology (COST). COST (www.cost.eu) is a funding agency for research and innovation networks. COST Actions help connect research initiatives across Europe and enable scientists to grow their ideas by sharing them with their peers. This boosts their research, career and innovation. PARENCHIMA (renalmri.org) is a community-driven Action in the COST program of the European Union, which unites more than 200 experts in renal MRI from 30 countries with the aim to improve the reproducibility and standardization of renal MRI biomarkers

Preclinical MRI of the kidney : methods and protocols

This Open Access volume provides readers with an open access protocol collection and wide-ranging recommendations for preclinical renal MRI used in translational research. The chapters in this book are interdisciplinary in nature and bridge the gaps between physics, physiology, and medicine. They are designed to enhance training in renal MRI sciences and improve the reproducibility of renal imaging research. Chapters provide guidance for exploring, using and developing small animal renal MRI in your laboratory as a unique tool for advanced in vivo phenotyping, diagnostic imaging, and research into potential new therapies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Preclinical MRI of the Kidney: Methods and Protocols is a valuable resource and will be of importance to anyone interested in the preclinical aspect of renal and cardiorenal diseases in the fields of physiology, nephrology, radiology, and cardiology. This publication is based upon work from COST Action PARENCHIMA, supported by European Cooperation in Science and Technology (COST). COST (www.cost.eu) is a funding agency for research and innovation networks. COST Actions help connect research initiatives across Europe and enable scientists to grow their ideas by sharing them with their peers. This boosts their research, career and innovation. PARENCHIMA (renalmri.org) is a community-driven Action in the COST program of the European Union, which unites more than 200 experts in renal MRI from 30 countries with the aim to improve the reproducibility and standardization of renal MRI biomarkers