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Nassar J, Trabelsi A, Amer R, Le Fur Y, Attarian S, Radunsky D, Blumenfeld-Katzir T, Greenspan H, Bendahan D, Ben-Eliezer N. Estimation of subvoxel fat infiltration in neurodegenerative muscle disorders using quantitative multi-T 2 analysis. NMR IN BIOMEDICINE 2023:e4947. [PMID: 37021657 DOI: 10.1002/nbm.4947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 02/13/2023] [Accepted: 03/21/2023] [Indexed: 06/19/2023]
Abstract
MRI's T2 relaxation time is a valuable biomarker for neuromuscular disorders and muscle dystrophies. One of the hallmarks of these pathologies is the infiltration of adipose tissue and a loss of muscle volume. This leads to a mixture of two signal components, from fat and from water, to appear in each imaged voxel, each having a specific T2 relaxation time. In this proof-of-concept work, we present a technique that can separate the signals from water and from fat within each voxel, measure their separate T2 values, and calculate their relative fractions. The echo modulation curve (EMC) algorithm is a dictionary-based technique that offers accurate and reproducible mapping of T2 relaxation times. We present an extension of the EMC algorithm for estimating subvoxel fat and water fractions, alongside the T2 and proton-density values of each component. To facilitate data processing, calf and thigh anatomy were automatically segmented using a fully convolutional neural network and FSLeyes software. The preprocessing included creating two signal dictionaries, for water and for fat, using Bloch simulations of the prospective protocol. Postprocessing included voxelwise fitting for two components, by matching the experimental decay curve to a linear combination of the two simulated dictionaries. Subvoxel fat and water fractions and relaxation times were generated and used to calculate a new quantitative biomarker, termed viable muscle index, and reflecting disease severity. This biomarker indicates the fraction of remaining muscle out of the entire muscle region. The results were compared with those using the conventional Dixon technique, showing high agreement (R = 0.98, p < 0.001). It was concluded that the new extension of the EMC algorithm can be used to quantify abnormal fat infiltration as well as identify early inflammatory processes corresponding to elevation in the T2 value of the water (muscle) component. This new ability may improve the diagnostic accuracy of neuromuscular diseases, help stratification of patients according to disease severity, and offer an efficient tool for tracking disease progression.
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Affiliation(s)
- Jannette Nassar
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | | | - Rula Amer
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | | | - Shahram Attarian
- Reference Center for Neuromuscular Diseases and ALS, La Timone University Hospital, Aix-Marseille University, Marseille, France
- Inserm, GMGF, Aix Marseille University, Marseille, France
| | - Dvir Radunsky
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | | | - Hayit Greenspan
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | | | - Noam Ben-Eliezer
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Center for Advanced Imaging Innovation and Research, New York University Langone Medical Center, New York, New York, USA
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Najac C, Boer VO, Kan HE, Webb AG, Ronen I. Improved detection limits of J-coupled neurometabolites in the human brain at 7 T with a J-refocused sLASER sequence. NMR IN BIOMEDICINE 2022; 35:e4801. [PMID: 35833462 PMCID: PMC9788253 DOI: 10.1002/nbm.4801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 07/02/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
In a standard spin echo, the time evolution due to homonuclear couplings is not reversed, leading to echo time (TE)-dependent modulation of the signal amplitude and signal loss in the case of overlapping multiplet resonances. This has an adverse effect on quantification of several important metabolites such as glutamate and glutamine. Here, we propose a J-refocused variant of the sLASER sequence (J-sLASER) to improve quantification of J-coupled metabolites at ultrahigh field (UHF). The use of the sLASER sequence is particularly advantageous at UHF as it minimizes chemical shift displacement error and results in relatively homogenous refocusing. We simulated the MRS signal from brain metabolites over a broad range of TE values with sLASER and J-sLASER, and showed that the signal of J-coupled metabolites was increased with J-sLASER with TE values up to ~80 ms. We further simulated "brain-like" spectra with both sequences at the shortest TE available on our scanner. We showed that, despite the slightly longer TE, the J-sLASER sequence results in significantly lower Cramer-Rao lower bounds (CRLBs) for J-coupled metabolites compared with those obtained with sLASER. Following phantom validation, we acquired spectra from two brain regions in 10 healthy volunteers (age 38 ± 15 years) using both sequences. We showed that using J-sLASER results in a decrease of CRLBs for J-coupled metabolites. In particular, we measured a robust ~38% decrease in the mean CRLB (glutamine) in parietal white matter and posterior cingulate cortex (PCC). We further showed, in 10 additional healthy volunteers (age 34 ± 15 years), that metabolite quantification following two separate acquisitions with J-sLASER in the PCC was repeatable. The improvement in quantification of glutamine may in turn improve the independent quantification of glutamate, the main excitatory neurotransmitter in the brain, and will simultaneously help to track possible modulations of glutamine, which is a key player in the glutamatergic cycle in astrocytes.
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Affiliation(s)
- Chloé Najac
- C. J. Gorter Center for High Field MRI, Department of RadiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Vincent O. Boer
- Danish Research Centre for Magnetic ResonanceCopenhagen University Hospital HvidovreHvidovreDenmark
| | - Hermien E. Kan
- C. J. Gorter Center for High Field MRI, Department of RadiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Andrew G. Webb
- C. J. Gorter Center for High Field MRI, Department of RadiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Itamar Ronen
- C. J. Gorter Center for High Field MRI, Department of RadiologyLeiden University Medical CenterLeidenThe Netherlands
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Kulpanovich A, Tal A. What is the optimal schedule for multiparametric MRS? A magnetic resonance fingerprinting perspective. NMR IN BIOMEDICINE 2021; 34:e4196. [PMID: 31814197 PMCID: PMC9244865 DOI: 10.1002/nbm.4196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 05/09/2023]
Abstract
Clinical magnetic resonance spectroscopy (MRS) mainly concerns itself with the quantification of metabolite concentrations. Metabolite relaxation values, which reflect the microscopic state of specific cellular and sub-cellular environments, could potentially hold additional valuable information, but are rarely acquired within clinical scan times. By varying the flip angle, repetition time and echo time in a preset way (termed a schedule), and matching the resulting signals to a pre-generated dictionary - an approach dubbed magnetic resonance fingerprinting - it is possible to encode the spins' relaxation times into the acquired signal, simultaneously quantifying multiple tissue parameters for each metabolite. Herein, we optimized the schedule to minimize the averaged root mean square error (RMSE) across all estimated parameters: concentrations, longitudinal and transverse relaxation time, and transmitter inhomogeneity. The optimal schedules were validated in phantoms and, subsequently, in a cohort of healthy volunteers, in a 4.5 mL parietal white matter single voxel and an acquisition time under 5 minutes. The average intra-subject, inter-scan coefficients of variation (CVs) for metabolite concentrations, T1 and T2 relaxation times were found to be 3.4%, 4.6% and 4.7% in-vivo, respectively, averaged over all major singlets. Coupled metabolites were quantified using the short echo time schedule entries and spectral fitting, and reliable estimates of glutamate+glutamine, glutathione and myo-inositol were obtained.
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Affiliation(s)
- Alexey Kulpanovich
- Department of Chemical Physics, Weizmann Institute of Science, 234 Herzel St., Rehovot 7610001, Israel
| | - Assaf Tal
- Department of Chemical Physics, Weizmann Institute of Science, 234 Herzel St., Rehovot 7610001, Israel
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Landheer K, Swanberg KM, Juchem C. Magnetic resonance Spectrum simulator (MARSS), a novel software package for fast and computationally efficient basis set simulation. NMR IN BIOMEDICINE 2021; 34:e4129. [PMID: 31313877 DOI: 10.1002/nbm.4129] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/01/2019] [Accepted: 05/17/2019] [Indexed: 06/10/2023]
Abstract
The aim of this study was to develop a novel software platform for the simulation of magnetic resonance spin systems, capable of simulating a large number of spatial points (1283 ) for large in vivo spin systems (up to seven coupled spins) in a time frame of the order of a few minutes. The quantum mechanical density-matrix formalism is applied, a coherence pathway filter is utilized for handling unwanted coherence pathways, and the 1D projection method, which provides a substantial reduction in computation time for a large number of spatial points, is extended to include sequences of an arbitrary number of RF pulses. The novel software package, written in MATLAB, computes a basis set of 23 different metabolites (including the two anomers of glucose, seven coupled spins) with 1283 spatial points in 26 min for a three-pulse experiment on a personal desktop computer. The simulated spectra are experimentally verified with data from both phantom and in vivo MEGA-sLASER experiments. Recommendations are provided regarding the various assumptions made when computing a basis set for in vivo MRS with respect to the number of spatial points simulated and the consideration of relaxation.
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Affiliation(s)
- Karl Landheer
- Biomedical Engineering, Columbia University Fu Foundation School of Engineering and Applied Science, New York, NY, USA
| | - Kelley M Swanberg
- Biomedical Engineering, Columbia University Fu Foundation School of Engineering and Applied Science, New York, NY, USA
| | - Christoph Juchem
- Biomedical Engineering, Columbia University Fu Foundation School of Engineering and Applied Science, New York, NY, USA
- Radiology, Columbia University College of Physicians and Surgeons, New York, NY, USA
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Increased Glutamate concentrations during prolonged motor activation as measured using functional Magnetic Resonance Spectroscopy at 3T. Neuroimage 2020; 223:117338. [DOI: 10.1016/j.neuroimage.2020.117338] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 01/20/2023] Open
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Kirov II, Tal A. Potential clinical impact of multiparametric quantitative MR spectroscopy in neurological disorders: A review and analysis. Magn Reson Med 2020; 83:22-44. [PMID: 31393032 PMCID: PMC6814297 DOI: 10.1002/mrm.27912] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/06/2019] [Accepted: 06/29/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE Unlike conventional MR spectroscopy (MRS), which only measures metabolite concentrations, multiparametric MRS also quantifies their longitudinal (T1 ) and transverse (T2 ) relaxation times, as well as the radiofrequency transmitter inhomogeneity (B1+ ). To test whether knowledge of these additional parameters can improve the clinical utility of brain MRS, we compare the conventional and multiparametric approaches in terms of expected classification accuracy in differentiating controls from patients with neurological disorders. THEORY AND METHODS A literature review was conducted to compile metabolic concentrations and relaxation times in a wide range of neuropathologies and regions of interest. Simulations were performed to construct receiver operating characteristic curves and compute the associated areas (area under the curve) to examine the sensitivity and specificity of MRS for detecting each pathology in each region. Classification accuracy was assessed using metabolite concentrations corrected using population-averages for T1 , T2 , and B1+ (conventional MRS); using metabolite concentrations corrected using per-subject values (multiparametric MRS); and using an optimal linear multiparametric estimator comprised of the metabolites' concentrations and relaxation constants (multiparametric MRS). Additional simulations were conducted to find the minimal intra-subject precision needed for each parameter. RESULTS Compared with conventional MRS, multiparametric approaches yielded area under the curve improvements for almost all neuropathologies and regions of interest. The median area under the curve increased by 0.14 over the entire dataset, and by 0.24 over the 10 instances with the largest individual increases. CONCLUSIONS Multiparametric MRS can substantially improve the clinical utility of MRS in diagnosing and assessing brain pathology, motivating the design and use of novel multiparametric sequences.
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Affiliation(s)
- Ivan I. Kirov
- Center for Advanced Imaging Innovation and Research (CAIR), Bernard and Irene Schwartz Center for Biomedical Imaging, New York University School of Medicine, Department of Radiology, 660 1 Avenue, New York, NY 10016, United States of America
| | - Assaf Tal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, 234 Herzel St., Rehovot 7610001, Israel
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Radunsky D, Blumenfeld-Katzir T, Volovyk O, Tal A, Barazany D, Tsarfaty G, Ben-Eliezer N. Analysis of magnetization transfer (MT) influence on quantitative mapping of T 2 relaxation time. Magn Reson Med 2019; 82:145-158. [PMID: 30860287 DOI: 10.1002/mrm.27704] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 12/22/2022]
Abstract
PURPOSE Multi-echo spin-echo (MESE) protocol is the most effective tool for mapping T2 relaxation in vivo. Still, MESE extensive use of radiofrequency pulses causes magnetization transfer (MT)-related bias of the water signal, instigated by the presence of macromolecules (MMP). Here, we analyze the effects of MT on MESE signal, alongside their impact on quantitative T2 measurements. METHODS Study used 3 models: in vitro urea phantom, ex vivo horse brain, and in vivo human brain. MT ratio (MTR) was measured between single-SE and MESE protocols under different scan settings including varying echo train lengths, number of slices, and inter-slice gap. MTR and T2 values were extracted for each model and protocol. RESULTS MT interactions biased MESE signals, and in certain settings, the corresponding T2 values. T2 underestimation of up to 4.3% was found versus single-SE values in vitro and up to 13.8% ex vivo, correlating with the MMP content. T2 bias originated from intra-slice saturation of the MMP, rather than from indirect saturation in multi-slice acquisitions. MT-related signal attenuation was caused by slice crosstalk and/or partial T1 recovery, whereas smaller contribution was caused by MMP interactions. Inter-slice gap had a similar effect on in vivo MTR (21.2%), in comparison to increasing the number of slices (18.9%). CONCLUSIONS MT influences MESE protocols either by uniformly attenuating the entire echo train or by cumulatively attenuating the signal along the train. Although both processes depend on scan settings and MMP content, only the latter will cause underestimation of T2 .
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Affiliation(s)
- Dvir Radunsky
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | | | - Osnat Volovyk
- Department of Chemical Physics, The Weizmann Institute, Rehovot, Israel
| | - Assaf Tal
- Department of Chemical Physics, The Weizmann Institute, Rehovot, Israel
| | - Daniel Barazany
- Strauss computational neuroimaging center, Tel Aviv University, Tel Aviv, Israel
| | - Galia Tsarfaty
- Department of Diagnostic Imaging, Sheba Medical Center, Ramat Gan, Israel
| | - Noam Ben-Eliezer
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.,Center for Advanced Imaging Innovation and Research (CAI2R), NewYork University Langone Medical Center, New York, New York
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Volovyk O, Tal A. Application of phase rotation to STRESS localization scheme at 3 T. Magn Reson Med 2017; 79:2481-2490. [PMID: 28972290 DOI: 10.1002/mrm.26911] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/10/2017] [Accepted: 08/17/2017] [Indexed: 12/26/2022]
Abstract
PURPOSE Application of phase rotation to the STRESS (=STEAM+PRESS) localization scheme, to shorten echo time, minimize J-coupling dephasing and estimate B1+ inhomogeneity. STRESS (=STEAM + PRESS) simultaneously refocuses and acquires the double spin echo (SE123 ) and stimulated echo (STE- ) pathways, combining PRESS-like signal with lower chemical shift displacement as in STEAM. Phase rotation effectively separates coherence pathways, allows reduction of spoiling gradients moments leading to reduction in echo time. Implementing it in STRESS allows one to individually phase-correct SE123 and STE- prior to combination. Moreover, B1+ inhomogeneity can be assessed by comparing the measured ratio of resonance intensities of SE123 and STE- pathways to the simulated one. METHODS In vivo spectra were acquired from a single voxel placed in the sensory-motor cortex of 10 healthy volunteers, using phase rotation-STRESS/PRESS/STEAM sequences at 3 T scanner. The phases of each slice-selective pulse were incremented by Δϕ1/2/3=22.5°/-45°/45°. RESULTS Phase rotation-STRESS showed quantification accuracy (% Cramer Rao lower bounds) and reproducibility (% coefficients of variation) comparable to PRESS and STEAM, in both phantoms and in vivo study. Minimal echo time achieved was 13 ms. CONCLUSION Phase rotation complements STRESS by reducing echo time, allowing processing of each pathway individually prior to addition and providing B1+ estimation in single voxel proton magnetic resonance spectroscopy. Magn Reson Med 79:2481-2490, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Osnat Volovyk
- Chemical Physics Department, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Tal
- Chemical Physics Department, Weizmann Institute of Science, Rehovot, Israel
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