arXiv subjects

Matthew S. Rosen

Publications and source records attributed to Matthew S. Rosen.

34 records · Page 2Linked to original sources

arXiv2022

Accurate super-resolution low-field brain MRI

The recent introduction of portable, low-field MRI (LF-MRI) into the clinical setting has the potential to transform neuroimaging. However, LF-MRI is limited by lower resolution and signal-to-noise ratio, leading to incomplete characterization of brain regions. To address this challenge, recent advances in machine learning facilitate the synthesis of higher resolution images derived from one or multiple lower resolution scans. Here, we report the extension of a machine learning super-resolution (SR) algorithm to synthesize 1 mm isotropic MPRAGE-like scans from LF-MRI T1-weighted and T2-weighted sequences. Our initial results on a paired dataset of LF and high-field (HF, 1.5T-3T) clinical scans show that: (i) application of available automated segmentation tools directly to LF-MRI images falters; but (ii) segmentation tools succeed when applied to SR images with high correlation to gold standard measurements from HF-MRI (e.g., r = 0.85 for hippocampal volume, r = 0.84 for the thalamus, r = 0.92 for the whole cerebrum). This work demonstrates proof-of-principle post-processing image enhancement from lower resolution LF-MRI sequences. These results lay the foundation for future work to enhance the detection of normal and abnormal image findings at LF and ultimately improve the diagnostic performance of LF-MRI. Our tools are publicly available on FreeSurfer (surfer.nmr.mgh.harvard.edu/).

eess.IV↗

arXiv2021

NMR of $^{31}$P Nuclear Spin Singlet States in Organic Diphosphates

$^{31}$P NMR and MRI are commonly used to study organophosphates that are central to cellular energy metabolism. In some molecules of interest, such as adenosine diphosphate (ADP) and nicotinamide adenine dinucleotide (NAD), pairs of coupled $^{31}$P nuclei in the diphosphate moiety should enable the creation of nuclear spin singlet states, which may be long-lived and can be selectively detected via quantum filters. Here, we show that $^{31}$P singlet states can be created on ADP and NAD, but their lifetimes are shorter than T$_{1}$ and are strongly sensitive to pH. Nevertheless, the singlet states were used with a quantum filter to successfully isolate the $^{31}$P NMR spectra of those molecules from the adenosine triphosphate (ATP) background signal.

physics.chem-ph↗

arXiv2021

An End-to-End AI-Based Framework for Automated Discovery of CEST/MT MR Fingerprinting Acquisition Protocols and Quantitative Deep Reconstruction (AutoCEST)

Purpose: To develop an automated machine-learning-based method for the discovery of rapid and quantitative chemical exchange saturation transfer (CEST) MR fingerprinting acquisition and reconstruction protocols. Methods: An MR physics governed AI system was trained to generate optimized acquisition schedules and the corresponding quantitative reconstruction neural-network. The system (termed AutoCEST) is composed of a CEST saturation block, a spin dynamics module, and a deep reconstruction network, all differentiable and jointly connected. The method was validated using a variety of chemical exchange phantoms and an in-vivo mouse brain at 9.4T. Results: The acquisition times for AutoCEST optimized schedules ranged from 35-71s, with a quantitative image reconstruction time of only 29 ms. The resulting exchangeable proton concentration maps for the phantoms were in good agreement with the known solute concentrations for AutoCEST sequences (mean absolute error = 2.42 mM; Pearson's r=0.992 , p$<$0.0001), but not for an unoptimized sequence (mean absolute error = 65.19 mM; Pearson's r=-0.161, p=0.522). Similarly, improved exchange rate agreement was observed between AutoCEST and quantification of exchange using saturation power (QUESP) methods (mean absolute error: 35.8 Hz, Pearson's r=0.971, p$<$0.0001) compared to an unoptimized schedule and QUESP (mean absolute error = 58.2 Hz; Pearson's r=0.959, p$<$0.0001). The AutoCEST in-vivo mouse brain semi-solid proton volume-fractions were lower in the cortex (12.21$\pm$1.37%) compared to the white-matter (19.73 $\pm$ 3.30%), as expected, and the amide proton volume-fraction and exchange rates agreed with previous reports. Conclusion: AutoCEST can automatically generate optimized CEST/MT acquisition protocols that can be rapidly reconstructed into quantitative exchange parameter maps.

physics.med-ph↗

arXiv2021

Two-Orders-of-Magnitude Improvement in the Total Spin Angular Momentum of 131Xe Nuclei Using Spin Exchange Optical Pumping

We report on hyperpolarization of quadrupolar (I=3/2) 131Xe via spin-exchange optical pumping. Observations of the 131Xe polarization dynamics show that the effective alkali-metal/131Xe spin-exchange cross-sections are large enough to compete with 131Xe spin relaxation. 131Xe polarization up to 7.6 p/m 1.5 percent was achieved in ca. 8.5EE20 spins--a ca. 100-fold improvement in the total spin angular momentum--enabling applications including measurement of spin-dependent neutron-131Xe s-wave scattering and sensitive searches for time-reversal violation in neutron-131Xe interactions beyond the Standard Model.

physics.atom-ph↗

arXiv2021

Homonuclear J-Coupling Spectroscopy at Low Magnetic Fields using Spin-Lock Induced Crossing

Nuclear magnetic resonance (NMR) spectroscopy usually requires high magnetic fields to create spectral resolution among different proton species. At low fields, chemical shift dispersion is insufficient to separate the species, and the spectrum exhibits just a single line. In this work, we demonstrate that spectra can nevertheless be acquired at low field using a novel pulse sequence called spin-lock induced crossing (SLIC). This probes energy level crossings induced by a weak spin-locking pulse and produces a unique J-coupling spectrum for most organic molecules. Unlike other forms of low-field J-coupling spectroscopy, our technique does not require the presence of heteronuclei and can be used for most compounds in their native state. We performed SLIC spectroscopy on a number of small molecules at 276 kHz and 20.8 MHZ, and we show that SLIC spectra can be simulated in good agreement with measurements.

physics.chem-ph↗

arXiv2020

Micron-scale SABRE-enhanced NV-NMR Spectroscopy

Optically-probed nitrogen-vacancy (NV) quantum defects in diamond can detect nuclear magnetic resonance (NMR) signals with high-spectral resolution from micron-scale sample volumes of about 10 picoliters. However, a key challenge for NV-NMR is detecting samples at millimolar concentrations. Here, we demonstrate an improvement in NV-NMR proton concentration sensitivity of about $10^5$ over thermal polarization by hyperpolarizing sample proton spins through signal amplification by reversible exchange (SABRE), enabling micron-scale NMR of small molecule sample concentrations as low as 1 millimolar in picoliter volumes. The SABRE-enhanced NV-NMR technique may enable detection and chemical analysis of low concentration molecules and their dynamics in complex micron-scale systems such as single-cells.

physics.app-ph↗

arXiv2020

A Portable Brain MRI Scanner for Underserved Settings and Point-Of-Care Imaging

Access to and availability of MRI scanners is typically limited by their cost, siting and infrastructure requirements. This precludes MRI diagnostics, the reference standard for neurological assessment, in patients who cannot be transported to specialized scanner suites. This includes patients who are critically ill and unstable, and patients located in low-resource settings. The scanner design presented here aims to extend the reach of MRI by substantially reducing these limitations. Our goal is to shift the cost-benefit calculation for MRI toward more frequent and varied use, including improved accessibility worldwide and point of care operation. Here, we describe a portable brain MRI scanner using a compact, lightweight permanent magnet, with a built-in readout field gradient. Our low-field (80 mT) Halbach cylinder design of rare-earth permanent magnets results in a 122 kg magnet with minimal stray-field, requiring neither cryogenics nor external power. The built-in magnetic field gradient reduces reliance on high-power gradient drivers, which not only lowers overall system power and cooling requirements, but also reduces acoustic noise. Imperfections in the encoding fields are mitigated with a generalized iterative image reconstruction technique, that uses prior characterization of the field patterns. Our system was validated using T1, T2 and proton density weighted in vivo brain images with a spatial resolution of 2.2 x 1.3 x 6.8 mm$^3$.

eess.IV↗

arXiv2019

CEST MR-Fingerprinting: practical considerations and insights for acquisition schedule design and improved reconstruction

Purpose: To understand the influence of various acquisition parameters on the ability of CEST MR-Fingerprinting (MRF) to discriminate different chemical exchange parameters and to provide tools for optimal acquisition schedule design and parameter map reconstruction. Methods: Numerical simulations were conducted using a parallel-computing implementation of the Bloch-McConnell equations, examining the effect of TR, TE, flip-angle, water T$_{1}$ and T$_{2}$, saturation-pulse duration, power, and frequency on the discrimination ability of CEST-MRF. A modified Euclidean-distance matching metric was evaluated and compared to traditional dot-product matching. L-Arginine phantoms of various concentrations and pH were scanned at 4.7T and the results compared to numerical findings. Results: Simulations for dot-product matching demonstrated that the optimal flip-angle and saturation times are 30$^{\circ}$ and 1100 ms, respectively. The optimal maximal saturation power was 3.4 $μ$T for concentrated solutes with a slow exchange-rate, and 5.2 $μ$T for dilute solutes with medium-to-fast exchange-rates. Using the Euclidean-distance matching metric, much lower maximum saturation powers were required (1.6 and 2.4 $μ$T, respectively), with a slightly longer saturation time (1500 ms) and 90$^{\circ}$ flip-angle. For both matching metrics, the discrimination ability increased with the repetition time. The experimental results were in agreement with simulations, demonstrating that more than a 50% reduction in scan-time can be achieved by Euclidean-distance-based matching. Conclusion: Optimization of the CEST-MRF acquisition schedule is critical for obtaining the best exchange parameter accuracy. The use of Euclidean-distance-based matching of signal trajectories simultaneously improved the discrimination ability and reduced the scan time and maximal saturation power required.

physics.med-ph↗

arXiv2018

MR fingerprinting Deep RecOnstruction NEtwork (DRONE)

PURPOSE: Demonstrate a novel fast method for reconstruction of multi-dimensional MR Fingerprinting (MRF) data using Deep Learning methods. METHODS: A neural network (NN) is defined using the TensorFlow framework and trained on simulated MRF data computed using the Bloch equations. The accuracy of the NN reconstruction of noisy data is compared to conventional MRF template matching as a function of training data size, and quantified in a both simulated numerical brain phantom data and acquired data from the ISMRM/NIST phantom. The utility of the method is demonstrated in a healthy subject in vivo at 1.5 T. RESULTS: Network training required 10 minutes and once trained, data reconstruction required approximately 10 ms. Reconstruction of simulated brain data using the NN resulted in a root-mean-square error (RMSE) of 3.5 ms for T1 and 7.8 ms for T2. The RMSE for the NN trained on sparse dictionaries was approximately 6 fold lower for T1 and 2 fold lower for T2 than conventional MRF dot-product dictionary matching on the same dictionaries. Phantom measurements yielded good agreement (R2=0.99) between the T1 and T2 estimated by the NN and reference values from the ISMRM/NIST phantom. CONCLUSION: Reconstruction of MRF data with a NN is accurate, 300 fold faster and more robust to noise and undersampling than conventional MRF dictionary matching.

cs.CV↗

arXiv2017

Rapid and Quantitative Chemical Exchange Saturation Transfer (CEST) Imaging with Magnetic Resonance Fingerprinting (MRF)

Purpose: To develop a fast magnetic resonance fingerprinting (MRF) method for quantitative chemical exchange saturation transfer (CEST) imaging. Methods: We implemented a CEST-MRF method to quantify the chemical exchange rate and volume fraction of the N$α$-amine protons of L-arginine (L-Arg) phantoms and the amide and semi-solid exchangeable protons of in vivo rat brain tissue. L-Arg phantoms were made with different concentrations (25-100 mM) and pH (pH 4-6). The MRF acquisition schedule varied the saturation power randomly for 30 iterations (phantom: 0-6 $μ$T; in vivo: 0-4 $μ$T) with a total acquisition time of <=2 minutes. The signal trajectories were pattern-matched to a large dictionary of signal trajectories simulated using the Bloch-McConnell equations for different combinations of exchange rate, exchangeable proton volume fraction, and water T1 and T2* relaxation times. Results: The chemical exchange rates of the N$α$-amine protons of L-Arg were significantly (p<0.0001) correlated with the rates measured with the Quantitation of Exchange using Saturation Power method. Similarly, the L-Arg concentrations determined using MRF were significantly (p<0.0001) correlated with the known concentrations. The pH dependence of the exchange rate was well fit (R2=0.9186) by a base catalyzed exchange model. The amide proton exchange rate measured in rat brain cortex (36.3+-12.9 Hz) was in good agreement with that measured previously with the Water Exchange spectroscopy method (28.6+-7.4 Hz). The semi-solid proton volume fraction was elevated in white (11.2+-1.7%) compared to gray (7.6+-1.8%) matter brain regions in agreement with previous magnetization transfer studies. Conclusion: CEST-MRF provides a method for fast, quantitative CEST imaging.

physics.med-ph↗

arXiv2017

Image reconstruction by domain transform manifold learning

Image reconstruction plays a critical role in the implementation of all contemporary imaging modalities across the physical and life sciences including optical, MRI, CT, PET, and radio astronomy. During an image acquisition, the sensor encodes an intermediate representation of an object in the sensor domain, which is subsequently reconstructed into an image by an inversion of the encoding function. Image reconstruction is challenging because analytic knowledge of the inverse transform may not exist a priori, especially in the presence of sensor non-idealities and noise. Thus, the standard reconstruction approach involves approximating the inverse function with multiple ad hoc stages in a signal processing chain whose composition depends on the details of each acquisition strategy, and often requires expert parameter tuning to optimize reconstruction performance. We present here a unified framework for image reconstruction, AUtomated TransfOrm by Manifold APproximation (AUTOMAP), which recasts image reconstruction as a data-driven, supervised learning task that allows a mapping between sensor and image domain to emerge from an appropriate corpus of training data. We implement AUTOMAP with a deep neural network and exhibit its flexibility in learning reconstruction transforms for a variety of MRI acquisition strategies, using the same network architecture and hyperparameters. We further demonstrate its efficiency in sparsely representing transforms along low-dimensional manifolds, resulting in superior immunity to noise and reconstruction artifacts compared with conventional handcrafted reconstruction methods. In addition to improving the reconstruction performance of existing acquisition methodologies, we anticipate accelerating the discovery of new acquisition strategies across modalities as the burden of reconstruction becomes lifted by AUTOMAP and learned-reconstruction approaches.

cs.CV↗

arXiv2016

Nanodiamond-enhanced MRI

Nanodiamonds are of interest as nontoxic substrates for targeted drug delivery and as highly biostable fluorescent markers for cellular tracking. Beyond optical techniques however, options for noninvasive imaging of nanodiamonds in vivo are severely limited. Here, we demonstrate that the Overhauser effect, a proton-electron double resonance technique developed to detect free radicals in vivo, can enable high contrast magnetic resonance imaging (MRI) of nanodiamonds in water at room temperature and ultra-low magnetic field. The technique transfers spin polarization from paramagnetic impurities at nanodiamond surfaces to $^1$H spins in the surrounding water solution, creating MRI contrast on-demand. We further examine the conditions required for maximum enhancement as well as the ultimate sensitivity of the technique. The ability to perform continuous hyperpolarization via the Overhauser mechanism, in combination with excellent in vivo stability, raises the possibility of performing noninvasive tracking of nanodiamonds over indefinitely long periods of time.

cond-mat.mes-hall↗

arXiv2015

Probing Scalar Coupling Differences via Long-Lived Singlet States

We probe small scalar coupling differences via the coherent interactions between two nuclear spin singlet states in organic molecules. We show that the spin-lock induced crossing (SLIC) technique enables the coherent transfer of singlet order between one spin pair and another. The transfer is mediated by the difference in cis and trans vicinal J couplings among the spins. By measuring the transfer rate, we calculate a J coupling difference of $8 \pm 2$ mHz in phenylalanine-glycine-glycine and $2.57 \pm 0.04$ Hz in glutamate. We also characterize a coherence between two singlet states in glutamate, which may enable the creation of a long-lived quantum memory.

quant-ph↗

arXiv2013

Preparation of Nuclear Spin Singlet States using Spin-Lock Induced Crossing

We introduce a broadly applicable technique to create nuclear spin singlet states in organic molecules and other many-atom systems. We employ a novel pulse sequence to produce a spin-lock induced crossing (SLIC) of the spin singlet and triplet energy levels, which enables triplet/singlet polarization transfer and singlet state preparation. We demonstrate the utility of the SLIC method by producing a long-lived nuclear spin singlet state on two strongly-coupled proton pairs in the tripeptide molecule phenylalanine-glycine-glycine dissolved in D2O, and by using SLIC to measure the J-couplings, chemical shift differences, and singlet lifetimes of the proton pairs. We show that SLIC is more efficient at creating nearly-equivalent nuclear spin singlet states than previous pulse sequence techniques, especially when triplet/singlet polarization transfer occurs on the same timescale as spin-lattice relaxation.

quant-ph↗

arXiv2012

Dependence of nuclear spin singlet lifetimes on RF spin-locking power

We measure the lifetime of long-lived nuclear spin singlet states as a function of the strength of the RF spin-locking field and present a simple theoretical model that agrees well with our measurements, including the low-RF-power regime. We also measure the lifetime of a long-lived coherence between singlet and triplet states that does not require a spin-locking field for preservation. Our results indicate that for many molecules, singlet states can be created using weak RF spin-locking fields: more than two orders of magnitude lower RF power than in previous studies. Our findings suggest that in many biomolecules, singlets and related states with enhanced lifetimes might be achievable in vivo with safe levels of RF power.

physics.chem-ph↗

arXiv2006

Noninvasive measurements of gas exchange in a three-dimensional fluidized bed using hyperpolarized 129Xe NMR

We present a novel NMR technique that provides a non-invasive, direct measurement of gas exchange in a three-dimensional gas-fluidized bed of solid particles. The NMR spectrum of hyperpolarized 129Xe gas in an Al2O3 particle bed displays three resolved peaks corresponding to xenon in bubbles, the interstitial spaces (emulsion), and adsorbed on particles. Modified NMR exchange and saturation-recovery sequences, together with data analysis based on an exchange-coupled set of Bloch equations, yield gas exchange rate constants between the emulsion and adsorbed phases, and between the bubble and emulsion phases. The results are in approximate agreement previously unverified predictions from well-known models of fluidized bed behavior. Incorporation of NMR imaging methodologies would straightforwardly allow similar measurements on a spatially-resolved basis.

cond-mat.mtrl-sci↗