Pulse Sequence Design Research Articles

Natural history data for young subjects with Sanfilippo syndrome type B (MPS IIIB)

Among the tools of structural biology, NMR spectroscopy is unique in that it not only derives a static three-dimensional structure, but also provides an atomic-level description of the local fluctuations and global dynamics around this static structure. A battery of NMR experiments is now available to probe the motions of proteins and nucleic acids over the whole biologically relevant timescale from picoseconds to hours. Here we focus on one of these methods, relaxation dispersion, which resolves dynamics on the micro- to millisecond timescale. Key biological processes that occur on this timescale include enzymatic catalysis, ligand binding, and local folding. In other words, relaxation-dispersion-resolved dynamics are often closely related to the function of the molecule and therefore highly interesting to the structural biochemist. With an astounding sensitivity of ∼0.5%, the method detects low-population excited states that are invisible to any other biophysical method. The kinetics of the exchange between the ground state and excited states are quantified in the form of the underlying exchange rate, while structural information about the invisible excited state is obtained in the form of its chemical shift. Lastly, the population of the excited state can be derived. This diversity in the information that can be obtained makes relaxation dispersion an excellent method to study the detailed mechanisms of conformational transitions and molecular interactions. Here we describe the two branches of relaxation dispersion, R2 and R1ρ, discussing their applicability, similarities, and differences, as well as recent developments in pulse sequence design and data processing.

Simulation-based quantification of native T1 and T2 of the myocardium using a modified MOLLI scheme and the importance of Magnetization Transfer

Quantitative cardiovascular Magnetic Resonance Imaging techniques are gaining wide acceptance within the MR community due to their potential to diagnose non-localized disease, guide therapy and improve patient outcome. During the last decade, there has been an increasing interest for developing new techniques that allow for simultaneous quantification of both T1 and T2 maps of myocardium. Newer studies demonstrated that the incorporation of MRI simulations could yield similar results to conventional mapping techniques in the myocardium. However, these simulation-based quantitative MR techniques usually compare the in-vivo T1 estimates against less accurate T1 techniques, whereas they present inconsistencies between simulation studies, phantom and in-vivo measurements. Moreover, these studies do not investigate the effect of Magnetization Transfer on the myocardial T1 and T2 estimates but are usually validated on phantoms where the MT effect is small.The main aim of this study was to perform simultaneous mapping of the native T1 and T2 of the myocardium through the utilization of a modified MOLLI pulse sequence and the incorporation of advanced MR simulations through the SQUAREMR framework. A second aim of this study was to investigate the effect of MT on simulation-based quantitative MR techniques.A conventional MOLLI pulse sequence was modified so as to present combined high T2 sensitivity and low MT effect. The new technique was applied in healthy volunteers and demonstrated an improved T1 accuracy compared to the conventional MOLLI and a T2 accuracy similar to the one provided by the T2prep-bSSFP method. The effect of MT on T1 and T2 estimates was also investigated in the current study. Phantoms with an increasing MT effect as well as phantoms without an MT effect were included in this work whereas several variants of the modified-MOLLI that introduce different amounts of T2 modulation on the MR signal and induce different MT effects were applied on the phantoms.The proposed simulation-based quantitative MR technique for simultaneous T1 and T2 mapping of the myocardium does not require the incorporation of a complicated custom designed pulse sequence and does not require a complicated reconstruction workflow. Moreover, the current study demonstrates for the first time that MT plays an important role in the simulation-based quantitative MR studies and points out the necessity of incorporating the study of MT in future techniques.

Exact broadband excitation of two-level systems by mapping spins to springs

Designing accurate and high-fidelity broadband pulses is an essential component in conducting quantum experiments across fields from protein spectroscopy to quantum optics. However, constructing exact and analytic broadband pulses remains unsolved due to the nonlinearity and complexity of the underlying spin system dynamics. Here, we present a nontrivial dynamic connection between nonlinear spin and linear spring systems and show the surprising result that such nonlinear and complex pulse design problems are equivalent to designing controls to steer linear harmonic oscillators under optimal forcing. We derive analytic broadband π/2 and π pulses that perform exact, or asymptotically exact, excitation and inversion over a defined bandwidth, and also with bounded amplitude. This development opens up avenues for pulse sequence design and lays a foundation for understanding the control of two-level systems.

Detection of Correlated Protein Backbone and Side-Chain Angle Fluctuations.

NMR methods for the characterization of local protein motions have attained a high level of sophistication. Measurement of the synchronization between those motions, however, poses a serious challenge. Such correlated motions are one of the underlying mechanisms for the propagation of local changes to remote sites and as such for information transfer. Here, we demonstrate the experimental detection of the synchronization of motion over an intermediate range. To that purpose, we designed pulse sequences for the measurement of cross-correlated relaxation between the backbone HN -N and side-chain Hβ -Cβ dipoles in Ile, Thr, and Val in the protein GB3. These bonds are related through two and three intervening dihedral angles. We show that the correlated motions inherent in a structural ensemble obtained from a large and diverse array of NMR probes are in excellent agreement with our measurements.

Linking the rotation of a rigid body to the Schr\xf6dinger equation: The quantum tennis racket effect and beyond

The design of efficient and robust pulse sequences is a fundamental requirement in quantum control. Numerical methods can be used for this purpose, but with relatively little insight into the control mechanism. Here, we show that the free rotation of a classical rigid body plays a fundamental role in the control of two-level quantum systems by means of external electromagnetic pulses. For a state to state transfer, we derive a family of control fields depending upon two free parameters, which allow us to adjust the efficiency, the time and the robustness of the control process. As an illustrative example, we consider the quantum analog of the tennis racket effect, which is a geometric property of any classical rigid body. This effect is demonstrated experimentally for the control of a spin 1/2 particle by using techniques of Nuclear Magnetic Resonance. We also show that the dynamics of a rigid body can be used to implement one-qubit quantum gates. In particular, non-adiabatic geometric quantum phase gates can be realized based on the Montgomery phase of a rigid body. The robustness issue of the gates is discussed.

Generalized min-max bound-based MRI pulse sequence design framework for wide-range T1 relaxometry: A case study on the tissue specific imaging sequence

This paper proposes a new design strategy for optimizing MRI pulse sequences for T1 relaxometry. The design strategy optimizes the pulse sequence parameters to minimize the maximum variance of unbiased T1 estimates over a range of T1 values using the Cramér-Rao bound. In contrast to prior sequences optimized for a single nominal T1 value, the optimized sequence using our bound-based strategy achieves improved precision and accuracy for a broad range of T1 estimates within a clinically feasible scan time. The optimization combines the downhill simplex method with a simulated annealing process. To show the effectiveness of the proposed strategy, we optimize the tissue specific imaging (TSI) sequence. Preliminary Monte Carlo simulations demonstrate that the optimized TSI sequence yields improved precision and accuracy over the popular driven-equilibrium single-pulse observation of T1 (DESPOT1) approach for normal brain tissues (estimated T1 700–2000 ms at 3.0T). The relative mean estimation error (MSE) for T1 estimation is less than 1.7% using the optimized TSI sequence, as opposed to less than 7.0% using DESPOT1 for normal brain tissues. The optimized TSI sequence achieves good stability by keeping the MSE under 7.0% over larger T1 values corresponding to different lesion tissues and the cerebrospinal fluid (up to 5000 ms). The T1 estimation accuracy using the new pulse sequence also shows improvement, which is more pronounced in low SNR scenarios.

Quantitative sodium MR imaging: A review of its evolving role in medicine

Sodium magnetic resonance (MR) imaging in humans has promised metabolic information that can improve medical management in important diseases. This technology has yet to find a role in clinical practice, lagging proton MR imaging by decades. This review covers the literature that demonstrates that this delay is explained by initial challenges of low sensitivity at low magnetic fields and the limited performance of gradients and electronics available in the 1980s. These constraints were removed by the introduction of 3T and now ultrahigh (≥7T) magnetic field scanners with superior gradients and electronics for proton MR imaging. New projection pulse sequence designs have greatly improved sodium acquisition efficiency. The increased field strength has provided the expected increased sensitivity to achieve resolutions acceptable for metabolic interpretation even in small target tissues. Consistency of quantification of the sodium MR image to provide metabolic parametric maps has been demonstrated by several different pulse sequences and calibration procedures. The vital roles of sodium ion in membrane transport and the extracellular matrix will be reviewed to indicate the broad opportunities that now exist for clinical sodium MR imaging. The final challenge is for the technology to be supplied on clinical ≥3T scanners.

Theoretical Description of Pulsed RYDMR: Refocusing Zero-Quantum and Single Quantum Coherences

Abstract A theoretical description of pulsed reaction yield detected magnetic resonance (RYDMR) is proposed. In RYDMR, magnetic resonance spectra of radical pairs (RPs) are indirectly detected by monitoring their recombination yield. Such a detection method is significantly more sensitive than conventional electron paramagnetic resonance (EPR), but design of appropriate pulse sequences for RYDMR requires additional effort because of a different observable. In this work various schemes for generating spin-echo like signals and detecting them by RYDMR are treated. Specifically, we consider refocusing of zero-quantum coherences (ZQCs) and single-quantum coherences (SQCs) by selective as well as by non-selective pulses and formulate a general analytical approach to pulsed RYDMR, which makes an efficient use of the product operator formalism. We anticipate that these results are of importance for RYDMR studies of elusive paramagnetic particles, notably, in organic semiconductors.

Reproducibility of quantitative indices of lung function and microstructure from 129 Xe chemical shift saturation recovery (CSSR) MR spectroscopy.

PurposeTo evaluate the reproducibility of indices of lung microstructure and function derived from 129Xe chemical shift saturation recovery (CSSR) spectroscopy in healthy volunteers and patients with chronic obstructive pulmonary disease (COPD), and to study the sensitivity of CSSR‐derived parameters to pulse sequence design and lung inflation level.MethodsPreliminary data were collected from five volunteers on three occasions, using two implementations of the CSSR sequence. Separately, three volunteers each underwent CSSR at three different lung inflation levels. After analysis of these preliminary data, five COPD patients were scanned on three separate days, and nine age‐matched volunteers were scanned three times on one day, to assess reproducibility.ResultsCSSR‐derived alveolar septal thickness (ST) and surface‐area‐to‐volume (S/V) ratio values decreased with lung inflation level (P < 0.001; P = 0.057, respectively). Intra‐subject standard deviations of ST were lower than the previously measured differences between volunteers and subjects with interstitial lung disease. The mean coefficient of variation (CV) values of ST were 3.9 ± 1.9% and 6.0 ± 4.5% in volunteers and COPD patients, respectively, similar to CV values for whole‐lung carbon monoxide diffusing capacity. The mean CV of S/V in volunteers and patients was 14.1 ± 8.0% and 18.0 ± 19.3%, respectively.Conclusion 129Xe CSSR presents a reproducible method for estimation of alveolar septal thickness. Magn Reson Med 77:2107–2113, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

TH‐F‐202‐02: Current Applications of MRI in Radiotherapy

MRI has excellent soft tissue contrast and can provide both anatomical and physiological information. It is becoming increasingly important in radiation therapy for treatment planning, image‐guided radiation therapy, and treatment assessment. It is critically important at this time point to educate and update our medical physicists about MRI to prepare for the upcoming surge of MRI applications in radiation therapy. This session will review important basics of MR physics, pulse sequence designs, and current radiotherapy application, as well as showcase exciting new developments in MRI that can be potentially useful in radiation therapy. Learning Objectives: To learn basics of MR physics and understand the differences between various pulse sequences To review current applications of MRI in radiation therapy.To discuss recent MRI advances for future MRI guided radiation therapyPartly supported by NIH (1R21CA165384).; W. Miller, Research supported in part by Siemens Healthcare; G. Li, My clinical research is in part supported by NIH U54CA137788. I have a collaborative research project with Philips Healthcare.; J. Cai, jing cai

TH‐F‐202‐03: Advances in MRI for Radiation Therapy

MRI has excellent soft tissue contrast and can provide both anatomical and physiological information. It is becoming increasingly important in radiation therapy for treatment planning, image‐guided radiation therapy, and treatment assessment. It is critically important at this time point to educate and update our medical physicists about MRI to prepare for the upcoming surge of MRI applications in radiation therapy. This session will review important basics of MR physics, pulse sequence designs, and current radiotherapy application, as well as showcase exciting new developments in MRI that can be potentially useful in radiation therapy. Learning Objectives: To learn basics of MR physics and understand the differences between various pulse sequences To review current applications of MRI in radiation therapy.To discuss recent MRI advances for future MRI guided radiation therapyPartly supported by NIH (1R21CA165384).; W. Miller, Research supported in part by Siemens Healthcare; G. Li, My clinical research is in part supported by NIH U54CA137788. I have a collaborative research project with Philips Healthcare.; J. Cai, jing cai

TH‐F‐202‐00: MRI for Radiation Therapy

MRI has excellent soft tissue contrast and can provide both anatomical and physiological information. It is becoming increasingly important in radiation therapy for treatment planning, image‐guided radiation therapy, and treatment assessment. It is critically important at this time point to educate and update our medical physicists about MRI to prepare for the upcoming surge of MRI applications in radiation therapy. This session will review important basics of MR physics, pulse sequence designs, and current radiotherapy application, as well as showcase exciting new developments in MRI that can be potentially useful in radiation therapy. Learning Objectives: To learn basics of MR physics and understand the differences between various pulse sequences To review current applications of MRI in radiation therapy.To discuss recent MRI advances for future MRI guided radiation therapyPartly supported by NIH (1R21CA165384).; W. Miller, Research supported in part by Siemens Healthcare; G. Li, My clinical research is in part supported by NIH U54CA137788. I have a collaborative research project with Philips Healthcare.; J. Cai, jing cai

TH‐F‐202‐01: MRI Basics

MRI has excellent soft tissue contrast and can provide both anatomical and physiological information. It is becoming increasingly important in radiation therapy for treatment planning, image‐guided radiation therapy, and treatment assessment. It is critically important at this time point to educate and update our medical physicists about MRI to prepare for the upcoming surge of MRI applications in radiation therapy. This session will review important basics of MR physics, pulse sequence designs, and current radiotherapy application, as well as showcase exciting new developments in MRI that can be potentially useful in radiation therapy. Learning Objectives: To learn basics of MR physics and understand the differences between various pulse sequences To review current applications of MRI in radiation therapy.To discuss recent MRI advances for future MRI guided radiation therapyPartly supported by NIH (1R21CA165384).; W. Miller, Research supported in part by Siemens Healthcare; G. Li, My clinical research is in part supported by NIH U54CA137788. I have a collaborative research project with Philips Healthcare.; J. Cai, jing cai

Triple quantum filtered spectroscopy of homonuclear three spin-1/2 systems employing isotropic mixing

We report the design and performance evaluation of novel pulse sequences for triple quantum filtered spectroscopy in homonuclear three spin-1/2 systems, employing isotropic mixing (IM) to excite triple quantum coherence (TQC). Our approach involves the generation of combination single quantum coherences (cSQC) from antisymmetric longitudinal or transverse magnetization components employing isotropic mixing (IM). cSQC’s are then converted to TQC by a selective 180° pulse on one of the spins. As IM ideally causes magnetization to evolve under the influence of the spin coupling Hamiltonian alone, TQC is generated at a faster rate compared to sequences involving free precession. This is expected to be significant when the spins have large relaxation rates. Our approach is demonstrated experimentally by TQC filtered 1D spectroscopy on a 1H AX2 system (propargyl bromide in the presence of a paramagnetic additive), as well as a 31P linear AMX system (ATP in agar gel). The performance of the IM-based sequences for TQC excitation are compared against the standard three pulse sequence (Ernst et al., 1987) and an AX2 spin pattern recognition sequence (Levitt and Ernst, 1983). The latter reaches the unitary bound on TQC preparation efficiency starting from thermal equilibrium in AX2 systems, not considering relaxation. It is shown that in systems where spins relax rapidly, the new IM-based sequences indeed perform significantly better than the above two known TQC excitation sequences, the sensitivity enhancement being especially pronounced in the case of the proton system investigated. An overview of the differences in relaxation behavior is presented for the different approaches. Applications are envisaged to Overhauser DNP experiments and to in vivo NMR.

Qubit Noise Spectroscopy for Non-Gaussian Dephasing Environments.

We introduce open-loop quantum control protocols for characterizing the spectral properties of non-Gaussian noise, applicable to both classical and quantum dephasing environments. By engineering a multidimensional frequency comb via repetition of suitably designed pulse sequences, the desired high-order spectra may be related to observable properties of the qubit probe. We prove that access to a high time resolution is key to achieving spectral reconstruction over an extended bandwidth, overcoming the limitations of existing schemes. Non-Gaussian spectroscopy is demonstrated for a classical noise model describing quadratic dephasing at an optimal point, as well as a quantum spin-boson model out of equilibrium. In both cases, we obtain spectral reconstructions that accurately predict the qubit dynamics in the non-Gaussian regime.

T1ρ MRI of healthy and fibrotic human livers at 1.5T.

BackgroundLiver fibrosis is a public health problem worldwide. There is a need of noninvasive imaging based methods for better diagnosis of this disease. In the current study, we aim to evaluate the potential of T1ρ MRI technique in detecting and characterizing different grades of liver fibrosis in vivo in humans.MethodsHealthy subjects and patients with liver fibrosis were prospectively recruited for T1ρ MRI of liver on a 1.5 T MR scanner. Single slice T1ρ weighted images were acquired at different spin lock duration (0, 10, 20 and 30 ms) with spin lock amplitude of 500 Hz in a single breath-hold. Additionally, liver’s T1ρ images were acquired from five healthy subjects on the same day (n = 2) and different day (n = 2) sessions for test–retest study. Liver biopsy samples from patients were obtained and used to calculate the METAVIR score to define the stage of fibrosis and inflammation grade. T1ρ maps were generated followed by computation of mean and standard deviation (SD) values. Coefficient of variation (COV) of T1ρ values between two MRI scans was computed to determine reproducibility in liver. T test was used to compare T1ρ values between healthy and fibrotic liver. Pearson correlation was performed between stages of liver fibrosis and T1ρ values.ResultsThe mean (SD) T1ρ value among subject with healthy liver was 51.04 (3.06) ms. The COV of T1ρ values between two repetitions in the same day session was 0.83 ± 0.8 % and in different day session was 5.4 ± 2.7 %. T1ρ values in fibrotic liver were significantly higher compared to those of healthy liver (p < 0.05). A statically significant correlation between stages of fibrosis and T1ρ values was observed (r = 0.99, p < 0.05). Inflammation score for one patient was 2 and for remaining patients it was 1.ConclusionsProposed T1ρ pulse sequence design and protocol enabled acquisition of a single slice T1ρ weighted images in a single breath-hold and hence mitigated breathing motion related artifacts. Preliminary results have shown the sensitivity of T1ρ values to changes induced by liver fibrosis, and may potentially be used as a clinical biomarker to delineate the stages of liver fibrosis. Further, studies on a large number of subjects are required to validate the observations of the current study. Nevertheless, T1ρ imaging can be easily setup on a clinical scanner to monitor the progression of liver fibrosis and to the evaluate efficacy of anti-fibrotic drugs.

Body MR Imaging: Artifacts, k-Space, and Solutions.

Body magnetic resonance (MR) imaging is challenging because of the complex interaction of multiple factors, including motion arising from respiration and bowel peristalsis, susceptibility effects secondary to bowel gas, and the need to cover a large field of view. The combination of these factors makes body MR imaging more prone to artifacts, compared with imaging of other anatomic regions. Understanding the basic MR physics underlying artifacts is crucial to recognizing the trade-offs involved in mitigating artifacts and improving image quality. Artifacts can be classified into three main groups: (a) artifacts related to magnetic field imperfections, including the static magnetic field, the radiofrequency (RF) field, and gradient fields; (b) artifacts related to motion; and (c) artifacts arising from methods used to sample the MR signal. Static magnetic field homogeneity is essential for many MR techniques, such as fat saturation and balanced steady-state free precession. Susceptibility effects become more pronounced at higher field strengths and can be ameliorated by using spin-echo sequences when possible, increasing the receiver bandwidth, and aligning the phase-encoding gradient with the strongest susceptibility gradients, among other strategies. Nonuniformities in the RF transmit field, including dielectric effects, can be minimized by applying dielectric pads or imaging at lower field strength. Motion artifacts can be overcome through respiratory synchronization, alternative k-space sampling schemes, and parallel imaging. Aliasing and truncation artifacts derive from limitations in digital sampling of the MR signal and can be rectified by adjusting the sampling parameters. Understanding the causes of artifacts and their possible solutions will enable practitioners of body MR imaging to meet the challenges of novel pulse sequence design, parallel imaging, and increasing field strength.

ChemInform Abstract: Broadband 1H Homodecoupled NMR Experiments: Recent Developments, Methods and Applications

AbstractReview: 155 refs.

Novel Magnetic Resonance Imaging Techniques in Brain Tumors.

Magnetic resonance imaging is a powerful, noninvasive imaging technique with exquisite sensitivity to soft tissue composition. Magnetic resonance imaging is primary tool for brain tumor diagnosis, evaluation of drug response assessment, and clinical monitoring of the patient during the course of their disease. The flexibility of magnetic resonance imaging pulse sequence design allows for a variety of image contrasts to be acquired, including information about magnetic resonance-specific tissue characteristics, molecular dynamics, microstructural organization, vascular composition, and biochemical status. The current review highlights recent advancements and novel approaches in MR characterization of brain tumors.

Broadband1H homodecoupled NMR experiments: Recent developments, methods and applications

In recent years, a great interest in the development of new broadband 1H homonuclear decoupled techniques providing simplified JHH multiplet patterns has emerged again in the field of small molecule NMR. The resulting highly*-resolved 1H NMR spectra display resonances as collapsed singlets, therefore minimizing signal overlap and expediting spectral analysis. Dr. Teodor Parella and Laura Castañar present a comprehensive compilation of the most recent advances in pure shift NMR spectroscopy, with a detailed discussion about the most relevant practical aspects in terms of pulse sequence design, selectivity, sensitivity, spectral resolution and performance. The implementation of the different reported strategies into traditional 1D and 2D NMR experiments is described and the combination with other complementary resolution-enhanced NMR techniques opens the door of the revolutionary concept of ultra high-resolved NMR spectroscopy. The usefulness of these novel techniques are illustrated for a number of challenging practical applications, such as the determination/ differentiation of very small chemical shift differences, analysis of highly crowded spectral regions, and the simplified and precise determination of relevant NMR parameters such as coupling constants, relaxation times or diffusion coefficients.