Accelerated phase-cycled SSFP imaging with compressed sensing

Balanced steady-state free precession (SSFP) imaging suffers from irrecoverable signal losses, known as banding artifacts, in regions of large B0 field inhomogeneity. A common solution is to acquire multiple phase-cycled images each with a different frequency sensitivity, such that the location of banding artifacts are shifted in space. These images are then combined to alleviate signal loss across the entire field-of-view. Although high levels of artifact suppression are viable using a large number of images, this is a time costly process that limits clinical utility. Here, we propose to accelerate individual acquisitions such that the overall scan time is equal to that of a single SSFP acquisition. Aliasing artifacts and noise are minimized by using a variable-density random sampling pattern in k-space, and by generating disjoint sampling patterns for separate acquisitions. A sparsity-enforcing method is then used for image reconstruction. Demonstrations on realistic brain phantom images, and in vivo brain and knee images are provided. In all cases, the proposed technique enables robust SSFP imaging in the presence of field inhomogeneities without prolonging scan times. © 2014 IEEE

Fat fraction mapping using bSSFP Signal Profile Asymmetries for Robust multi-Compartment Quantification (SPARCQ)

Purpose: To develop a novel quantitative method for detection of different tissue compartments based on bSSFP signal profile asymmetries (SPARCQ) and to provide a validation and proof-of-concept for voxel-wise water-fat separation and fat fraction mapping. Methods: The SPARCQ framework uses phase-cycled bSSFP acquisitions to obtain bSSFP signal profiles. For each voxel, the profile is decomposed into a weighted sum of simulated profiles with specific off-resonance and relaxation time ratios. From the obtained set of weights, voxel-wise estimations of the fractions of the different components and their equilibrium magnetization are extracted. For the entire image volume, component-specific quantitative maps as well as banding-artifact-free images are generated. A SPARCQ proof-of-concept was provided for water-fat separation and fat fraction mapping. Noise robustness was assessed using simulations. A dedicated water-fat phantom was used to validate fat fractions estimated with SPARCQ against gold-standard 1H MRS. Quantitative maps were obtained in knees of six healthy volunteers, and SPARCQ repeatability was evaluated in scan rescan experiments. Results: Simulations showed that fat fraction estimations are accurate and robust for signal-to-noise ratios above 20. Phantom experiments showed good agreement between SPARCQ and gold-standard (GS) fat fractions (fF(SPARCQ) = 1.02*fF(GS) + 0.00235). In volunteers, quantitative maps and banding-artifact-free water-fat-separated images obtained with SPARCQ demonstrated the expected contrast between fatty and non-fatty tissues. The coefficient of repeatability of SPARCQ fat fraction was 0.0512. Conclusion: The SPARCQ framework was proposed as a novel quantitative mapping technique for detecting different tissue compartments, and its potential was demonstrated for quantitative water-fat separation.Comment: 20 pages, 7 figures, submitted to Magnetic Resonance in Medicin

Profile-encoding reconstruction for multiple-acquisition balanced steady-state free precession imaging

Purpose: The scan-efficiency in multiple-acquisition balanced steady-state free precession imaging can be maintained by accelerating and reconstructing each phase-cycled acquisition individually, but this strategy ignores correlated structural information among acquisitions. Here, an improved acceleration framework is proposed that jointly processes undersampled data across N phase cycles. Methods: Phase-cycled imaging is cast as a profile-encoding problem, modeling each image as an artifact-free image multiplied with a distinct balanced steady-state free precession profile. A profile-encoding reconstruction (PE-SSFP) is employed to recover missing data by enforcing joint sparsity and total-variation penalties across phase cycles. PE-SSFP is compared with individual compressed-sensing and parallel-imaging (ESPIRiT) reconstructions. Results: In the brain and the knee, PE-SSFP yields improved image quality compared to individual compressed-sensing and other tested methods particularly for higher N values. On average, PE-SSFP improves peak SNR by 3.8 ± 3.0 dB (mean ± s.e. across N = 2–8) and structural similarity by 1.4 ± 1.2% over individual compressed-sensing, and peak SNR by 5.6 ± 0.7 dB and structural similarity by 7.1 ± 0.5% over ESPIRiT. Conclusion: PE-SSFP attains improved image quality and preservation of high-spatial-frequency information at high acceleration factors, compared to conventional reconstructions. PE-SSFP is a promising technique for scan-efficient balanced steady-state free precession imaging with improved reliability against field inhomogeneity. Magn Reson Med 78:1316–1329, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicin

Lung Imaging and Function Assessment using Non-Contrast-Enhanced Magnetic Resonance Imaging

Measurement of pulmonary ventilation and perfusion has significant clinical value for the diagnosis and monitoring of prevalent lung diseases. To this end, non-contrast-enhanced MRI techniques have emerged as a promising alternative to scintigraphical measurements, computed tomography, and contrast-enhanced MRI. Although these techniques allow the acquisition of both structural and functional information in the same scan session, they are prone to robustness issues related to imaging artifacts and post-processing techniques, limiting their clinical utilization. In this work, new acquisition and post-processing techniques were introduced for improving the robustness of non-contrast-enhanced MRI based functional lung imaging. Furthermore, pulmonary functional maps were acquired in 2-year-old congenital diaphragmatic hernia (CDH) patients to demonstrate the feasibility of non-contrast-enhanced MRI methods for functional lung imaging. In the first study, a multi-acquisition framework was developed to improve robustness against field inhomogeneity artifacts. This method was evaluated at 1.5T and 3T field strengths via acquisitions obtained from healthy volunteers. The results demonstrate that the proposed acquisition framework significantly improved ventilation map homogeneity p<0.05. In the second study, a post-processing method based on dynamic mode decomposition (DMD) was developed to accurately identify dominant spatiotemporal patterns in the acquisitions. This method was demonstrated on digital lung phantoms and in vivo acquisitions. The findings indicate that the proposed method led to a significant reduction in dispersion of estimated ventilation and perfusion map amplitudes across different number of measurements when compared with competing methods p<0.05. In the third study, the free-breathing non-contrast-enhanced dynamic acquisitions were obtained from 2-year-old patients after CDH repair, and then processed using the DMD to obtain pulmonary functional maps. Afterwards, functional differences between ipsilateral and contralateral lungs were assessed and compared with results obtained using contrast-enhanced MRI measurements. The results demonstrate that pulmonary ventilation and perfusion maps can be generated from dynamic acquisitions successfully without the need for ionizing radiation or contrast agents. Furthermore, lung perfusion parameters obtained with DMD MRI correlate very strongly with parameters obtained using dynamic contrast-enhanced MRI. In conclusion, the presented work improves the robustness and accuracy of non-contrast-enhanced functional lung imaging using MRI. Overall, the methods introduced in this work may serve as a valuable tool in the clinical adaptation of non-contrast-enhanced imaging methods and may be used for longitudinal assessments of pulmonary functional changes

Exploring configuration-based relaxometry and imaging with balanced steady-state free precession

Over the years, magnetic resonance (MR) imaging has become a fundamental part of the diagnostic process in hospitals worldwide. While the underlying physics dates back more than 60 years with the development of nuclear magnetic resonance, methods that aim to accurately measure the multitude of parameters governing the signal formation are still a topic of active research and developments today. The main aim of this work is to explore the possibilities of developing quantification techniques based on a particular type of MR acquisitions: balanced Steady-State Free Precession (bSSFP). The first chapter briefly introduces the most relevant basic concepts of MR physics that will serve as foundation for the development of the methods presented thereafter. In the second chapter, a new method using multiple bSSFP scans is presented that aim to achieve motion insensitive three-dimensional quantification of relaxation times and thereby improve a recently published technique based on unbalanced gradient echo acquisitions. The method is then evaluated both in phantoms and in vivo studies at 3 T and the results discussed. These include an interesting bias of the method that might provide useful insights into the underlying tissue micro-structure. One the major challenges with bSSFP imaging is the presence of dark regions inside the images, which are due to inhomogeneities in the main magnetic field. In the third chapter, a new approach to address those issues is proposed, termed trueCISS, which combines fast imaging using sparse sampling with compressed sensing reconstructions and multi-parametric fitting, which ultimately allows the synthesis of artefact-free images. Evaluation of the new method is done at 3 T for the human brain. Finally, an extension of the trueCISS technique is presented in chapter four, where the process used to model the data to the signal equation is replaced by a novel algorithm based on configuration theory, which is essentially a representation of the signal formation processes in the Fourier domain. The improved trueCISS imaging method is then successfully evaluated with measurements at ultra high field strengths such as 7 T and 9.4 T which demonstrate the advantages of the new approach

Steady-state anatomical and quantitative magnetic resonance imaging of the heart using RF-frequencymodulated techniques

Cardiovascular disease (CVD) is the leading cause of death in the United States and Europe and generates healthcare costs of hundreds of billions of dollars annually. Conventional methods of diagnosing CVD are often invasive and carry risks for the patient. For example, the gold standard for diagnosing coronary artery disease, a major class of CVD, is x-ray coronary angiography, which has the disadvantages of being invasive, being expensive, using ionizing radiation, and having a ris k of complications. Conversely, coronary MR angiography (MRA) does not use ionizing radiation, can effectively visualize tissues without the need for exogenous contrast agents, and benefits from an adaptable temporal resolution. However, the acquisition time of cardiac MRI is far longer than the temporal scales of cardiac and respiratory motion, necessitating some method of compensating for this motion. The free-running framework is a novel development in our lab, benefitting from advances over the past three decades, that attempts to address disadvantages of previous cardiac MRI approaches: it provides fully self-gated 5D cardiac MRI with a simplified workflow, improved ease-of-use, reduced operator dependence, and automatic patient-specific motion detection. Free-running imaging increases the amount of information available to the clinician and is flexible enough to be translated to different app lications within cardiac MRI. Moreover, the self-gating of the free-running framework decoupled the acquisition from the motion compensation and thereby opened up cardiac MRI to the wider class of steady-state-based techniques utilizing balanced steady-state free precession (bSSFP) sequences, which have the benefits of practical simplicity and high signal-to-noise ratio. The focus of this thesis was therefore on the application of steady- state techniques to cardiac MRI. The first part addressed the long acquisition time of the current free-running framework and focused on anatomical coronary imaging. The published protocol of the free- running framework used an interrupted bSSFP acquisition where CHESS fat saturation modules were inserted to provide blood-fat contrast, as they suppress the signal of fat tissue surrounding the coronary arteries, and were followed by ramp-up pulses to reduce artefacts arising from the return to steady-state. This interrupted acquisition, however, suffered from an interrupted steady-state, reduced time efficiency, and higher specific absorption rate (SAR). Using novel lipid-insensitive binomial off-resonant RF excitation (LIBRE) pulses developed in our lab, the first project showed that LIBRE pulses incorporated into an uninterrupted free-running bSSFP sequence could be successfully used for 5D cardiac MRI at 1.5T. The free-running LIBRE approach reduced the acquisition time and SAR relative to the previous interrupted approach while maintaining image quality and vessel conspicuity. Furthermore, this had been the first successful use of a fat-suppressing RF excitation pulse in an uninterrupted bSSFP sequence for cardiac imaging, demonstrating that uninterrupted bSSFP can be used for cardiac MRI and addressing the problem of clinical sequence availability. Inspired by the feasibility of uninterrupted bSSFP for cardiac MRI, the second part investigated the potential of PLANET, a novel 3D multiparametric mapping technique, for free-running 5D myocardial mapping. PLANET utilizes a phase-cycled bSSFP acquisition and a direct ellipse-fitting algorithm to calculate T1 and T2 relaxation times, which suggested that it could be readily integrated into the free-running framework without interrupting the steady-state. After initially calibrating the acquisition, the possibility of accelerating the static PLANET acquisition was explored prior to applying it to the moving heart. It was shown that PLANET accuracy and precision could be maintained with two-fold acceleration with a 3D Cartesian spiral trajectory, suggesting that PLANET for myocardial mapping with the free-running 5D radial acquisition is feasible. Further work should investigate optimizing the reconstruction scheme, improving the coil sensitivity estimate, and examining the use of the radial trajectory with a view to implementing free-running 5D myocardial T1 and T2 mapping. This thesis presents two approaches utilizing RF-frequency-modulated steady-state techniques for cardiac MRI. The first approach involved the novel application of an uninterrupted bSSFP acquisition with off-resonant RF excitation for anatomical coronary imaging. The second approach investigated the use of phase-cycled bSSFP for free-running 5D myocardial T1 and T2 mapping. Both methods addressed the challenge of clinical availability of sequences in cardiac MRI, by showing that a common and simple sequence like bSSFP can be used for acquisition while the steps of motion compensation and reconstruction can be handled offline, and thus have the potential to improve adoption of cardiac MRI. -- Les maladies cardiovasculaires (MCV) représentent la principale cause de décès aux États-Unis et en Europe et génèrent des coûts de santé de plusieurs centaines de milliards de dollars par an. Les méthodes conventionnelles de diagnostic des MCV sont souvent invasives et comportent des risques pour le patient. Par exemple, la méthode de référence pour le diagnostic de la maladie coronarienne, une catégorie majeure de MCV, est la coronarographie par rayons X qui a comme inconvénients son caractère invasif, son coût, l’utilisation de rayonnements ionisants et le risque de complications. A l’inverse, l'angiographie coronarienne par résonance magnétique (ARM) n'utilise pas de rayonnements ionisants, permet de visualiser efficacement les tissus sans avoir recours à des agents de contraste exogènes et bénéficie d'une résolution temporelle ajustable. Cependant, le temps d'acquisition en IRM cardiaque est bien plus long que les échelles temporelles des mouvements cardiaques et respiratoires en jeu, ce qui rend la compensation de ces mouvements indispensable. Le cadre dit de « free -running » est un nouveau développement de notre laboratoire qui bénéficie des progrès réalisés au cours des trois dernières décennies et tente de remédier aux inconvénients des approches précédentes pour l'IRM cardiaque : il fournit une IRM cardiaque en cinq dimensions (5D) complètement « self-gated » , c’est-à-dire capable de détecter les mouvements cardiaques et respiratoires, forte d’une implémentation simplifiée, d’une plus grande facilité d'utilisation, d’une dépendance réduite vis-à-vis de l'opérateur et d’une détection automatique des mouvements spécifiques du patient. L'imagerie « free- running » augmente la quantité d'informations à disposition du clinicien et est suffisamment flexible pour être appliquée à différents domaines de l'IRM cardiaque. De plus, le « self-gating » du cadre « free-running » a découplé l'acquisition de la compensation de mouvement et a ainsi ouvert l'IRM cardiaque à la classe plus large des techniques basées sur l'état stationnaire utilisant des séquences de précession libre équilibrée en état stationnaire (bSSFP), qui se distinguent par leur simplicité d’utilisation et leur rapport signal sur bruit élevé. Le thème de cette thèse est donc l'application des techniques basées sur l'état stationnaire à l'IRM cardiaque. La première partie porte sur le long temps d'acquisition de l'actuel cadre « free-running» et se concentre sur l'imagerie anatomique coronaire. Le protocole publié utilise une acquisition bSSFP interrompue où des modules de saturation de graisse (CHESS) sont insérés de façon à fournir un contraste sang-graisse puisqu’ils suppriment le signal du tissu graisseux entourant les artères coronaires, et sont suivis par des impulsions en rampe pour réduire les artefacts résultant du retour à l'état stable. Cette acquisition interrompue souffre cependant d'un état d'équilibre interrompu, d'une efficacité temporelle réduite et d'un débit d'absorption spécifique (DAS) plus élevé. En utilisant les nouvelles impulsions d'excitation radiofréquence (RF) binomiales hors -résonance insensibles aux lipides (LIBRE) développées dans notre laboratoi re, ce premier projet montre que les impulsions LIBRE incorporées dans une séquence bSSFP ininterrompue et « free-running » peuvent être utilisées avec succès pour l'IRM cardiaque 5D à 1,5 T. L'approche « free-running LIBRE » permet de réduire le temps d'acquisition et le DAS par rapport à l'approche interrompue précédente, tout en maintenant la perceptibilité des artères coronariennes. En outre, il s'agit de la première utilisation réussie d'une impulsion d'excitation RF supprimant la graisse dans une séquence bSSFP ininterrompue pour l'imagerie cardiaque, ce qui démontre le potentiel d’utilisation de la séquence bSSFP ininterrompue pour l'IRM cardiaque et résout le problème de la disponibilité de la séquence en clinique. Inspirée par la faisabilité d’utilisation de la séquence bSSFP ininterrompue pour l'IRM cardiaque, la deuxième partie étudie le potentiel de PLANET, une nouvelle technique de cartographie 3D multiparamétrique, pour la cartographie 5D du myocarde via l’imagerie « free-running ». PLANET utilise une acquisition bSSFP à cycle de phase et un algorithme d'ajustement d'ellipse direct pour calculer les temps de relaxation T1 et T2, ce qui suggère que cette méthode pourrait être facilement intégrée au cadre « free - running » sans interruption de l’état d'équilibre. Après calibration de l'acquisition, nous explorons la possibilité d'accélérer l'acquisition statique de PLANET pour l'appliquer au cœur. Nous démontrons que l'exactitude et la précision de PLANET peuvent être maintenues pour une accélération double avec une trajectoire 3D cartésienne en spirale, ce qui suggère que PLANET est réalisable pour la cartographie du myocarde avec une acquisition radiale 5D « free-running ». D'autres travaux devraient porter sur l'optimisation du schéma de reconstruction, l'amélioration de l'estimation de la sensibilité de l’antenne et l'examen de l'utilisation de la trajectoire radiale en vue de la mise en œuvre de la cartographie 5D « free-running » T1 et T2 du myocarde. Cette thèse présente deux approches utilisant des techniques de modulation de fréquence radio en état stationnaire pour l'IRM cardiaque. La première approche implique l'application nouvelle d'une acquisition bSSFP ininterrompue avec une excitation RF hors résonance pour l'imagerie anatomique coronaire. La seconde approche porte sur l'utilisation d’une séquence bSSFP à cycle de phase pour la cartographie 5D T1 et T2 du myocarde. Ces deux méthodes permettent de répondre au défi posé par la disponibilité des séquences en IRM cardiaque en montrant qu'une séquence commune et simple comme la bSSFP peut être utilisée pour l'acquisition, tandis que les étapes de compensation du mouvement et de reconstruction peuvent être traitées hors ligne. Ainsi, ces méthodes ont le potentiel de favoriser l'adoption de l'IRM cardiaque

Statistically segregated k-space sampling for accelerating multiple-acquisition MRI

A central limitation of multiple-acquisition magnetic resonance imaging (MRI) is the degradation in scan efficiency as the number of distinct datasets grows. Sparse recovery techniques can alleviate this limitation via randomly undersampled acquisitions. A frequent sampling strategy is to prescribe for each acquisition a different random pattern drawn from a common sampling density. However, naive random patterns often contain gaps or clusters across the acquisition dimension that in turn can degrade reconstruction quality or reduce scan efficiency. To address this problem, a statistically-segregated sampling method is proposed for multiple-acquisition MRI. This method generates multiple patterns sequentially, while adaptively modifying the sampling density to minimize k-space overlap across patterns. As a result, it improves incoherence across acquisitions while still maintaining similar sampling density across the radial dimension of k-space. Comprehensive simulations and in vivo results are presented for phase-cycled balanced steady-state free precession and multi-echo T2-weighted imaging. Segregated sampling achieves significantly improved quality in both Fourier and compressedsensing reconstructions of multiple-acquisition datasets

Physics-based Reconstruction Methods for Magnetic Resonance Imaging

Conventional Magnetic Resonance Imaging (MRI) is hampered by long scan times and only qualitative image contrasts that prohibit a direct comparison between different systems. To address these limitations, model-based reconstructions explicitly model the physical laws that govern the MRI signal generation. By formulating image reconstruction as an inverse problem, quantitative maps of the underlying physical parameters can then be extracted directly from efficiently acquired k-space signals without intermediate image reconstruction -- addressing both shortcomings of conventional MRI at the same time. This review will discuss basic concepts of model-based reconstructions and report about our experience in developing several model-based methods over the last decade using selected examples that are provided complete with data and code.Comment: 8 figures, review accepted to Philos. Trans. R. Soc.