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Ji B, Hosseini Z, Wang L, Zhou L, Tu X, Mao H. Spectral Wavelet-feature Analysis and Classification Assisted Denoising for enhancing magnetic resonance spectroscopy. NMR IN BIOMEDICINE 2021; 34:e4497. [PMID: 33751691 PMCID: PMC8969585 DOI: 10.1002/nbm.4497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 01/21/2021] [Accepted: 02/08/2021] [Indexed: 05/11/2023]
Abstract
Magnetic resonance spectroscopy (MRS) is capable of revealing important biochemical and metabolic information of tissues noninvasively. However, the low concentrations of metabolites often lead to poor signal-to-noise ratio (SNR) and a long acquisition time. Therefore, the applications of MRS in detection and quantitative measurements of metabolites in vivo remain limited. Reducing or even eliminating noise can improve SNR sufficiently to obtain high quality spectra in addition to increasing the number of signal averaging (NSA) or the field strength, both of which are limited in clinical applications. We present a Spectral Wavelet-feature ANalysis and Classification Assisted Denoising (SWANCAD) approach to differentiate signal and noise peaks in magnetic resonance spectra based on their respective wavelet features, followed by removing the identified noise components to improve SNR. The performance of this new denoising approach was evaluated by measuring and comparing SNRs and quantified metabolite levels of low NSA spectra (e.g. NSA = 8) before and after denoising using the SWANCAD approach or by conventional spectral fitting and denoising methods, such as LCModel and wavelet threshold methods, as well as the high NSA spectra (e.g. NSA = 192) recorded in the same sampling volumes. The results demonstrated that SWANCAD offers a more effective way to detect the signals and improve SNR by removing noise from the noisy spectra collected with low NSA or in the subminute scan time (e.g. NSA = 8 or 16 s). The potential applications of SWANCAD include using low NSA to accelerate MRS acquisition while maintaining adequate spectroscopic information for detection and quantification of the metabolites of interest when a limited time is available for an MRS examination in the clinical setting.
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Affiliation(s)
- Bing Ji
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, Georgia, The United States of America
| | - Zahra Hosseini
- MR R&D Collaborations, Siemens Medical Solutions Inc., Atlanta, Georgia, The United States of America
| | - Liya Wang
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, Georgia, The United States of America
- Department of Radiology, The People’s Hospital of Longhua, Shenzhen, Guangdong, China
| | - Lei Zhou
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, Georgia, The United States of America
| | - Xinhua Tu
- School of Communication and Information Engineering, Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu, China
| | - Hui Mao
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, Georgia, The United States of America
- To whom correspondence should be addressed: Hui Mao, PhD, Department of Radiology and Imaging Sciences, Emory University School of Medicine, 1841 Clifton Road NE, Atlanta, GA 30329, Tel: 404-712-0357, Fax: 404-712-5689,
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Wilson M, Andronesi O, Barker PB, Bartha R, Bizzi A, Bolan PJ, Brindle KM, Choi IY, Cudalbu C, Dydak U, Emir UE, Gonzalez RG, Gruber S, Gruetter R, Gupta RK, Heerschap A, Henning A, Hetherington HP, Huppi PS, Hurd RE, Kantarci K, Kauppinen RA, Klomp DWJ, Kreis R, Kruiskamp MJ, Leach MO, Lin AP, Luijten PR, Marjańska M, Maudsley AA, Meyerhoff DJ, Mountford CE, Mullins PG, Murdoch JB, Nelson SJ, Noeske R, Öz G, Pan JW, Peet AC, Poptani H, Posse S, Ratai EM, Salibi N, Scheenen TWJ, Smith ICP, Soher BJ, Tkáč I, Vigneron DB, Howe FA. Methodological consensus on clinical proton MRS of the brain: Review and recommendations. Magn Reson Med 2019; 82:527-550. [PMID: 30919510 PMCID: PMC7179569 DOI: 10.1002/mrm.27742] [Citation(s) in RCA: 235] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/01/2019] [Accepted: 02/25/2019] [Indexed: 12/14/2022]
Abstract
Proton MRS (1 H MRS) provides noninvasive, quantitative metabolite profiles of tissue and has been shown to aid the clinical management of several brain diseases. Although most modern clinical MR scanners support MRS capabilities, routine use is largely restricted to specialized centers with good access to MR research support. Widespread adoption has been slow for several reasons, and technical challenges toward obtaining reliable good-quality results have been identified as a contributing factor. Considerable progress has been made by the research community to address many of these challenges, and in this paper a consensus is presented on deficiencies in widely available MRS methodology and validated improvements that are currently in routine use at several clinical research institutions. In particular, the localization error for the PRESS localization sequence was found to be unacceptably high at 3 T, and use of the semi-adiabatic localization by adiabatic selective refocusing sequence is a recommended solution. Incorporation of simulated metabolite basis sets into analysis routines is recommended for reliably capturing the full spectral detail available from short TE acquisitions. In addition, the importance of achieving a highly homogenous static magnetic field (B0 ) in the acquisition region is emphasized, and the limitations of current methods and hardware are discussed. Most recommendations require only software improvements, greatly enhancing the capabilities of clinical MRS on existing hardware. Implementation of these recommendations should strengthen current clinical applications and advance progress toward developing and validating new MRS biomarkers for clinical use.
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Affiliation(s)
- Martin Wilson
- Centre for Human Brain Health and School of Psychology, University of Birmingham, Birmingham, England
| | - Ovidiu Andronesi
- Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Peter B Barker
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Robert Bartha
- Robarts Research Institute, University of Western Ontario, London, Canada
| | - Alberto Bizzi
- U.O. Neuroradiologia, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Patrick J Bolan
- Department of Radiology, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota
| | - Kevin M Brindle
- Department of Biochemistry, University of Cambridge, Cambridge, England
| | - In-Young Choi
- Department of Neurology, Hoglund Brain Imaging Center, University of Kansas Medical Center, Kansas City, Kansas
| | - Cristina Cudalbu
- Center for Biomedical Imaging, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Ulrike Dydak
- School of Health Sciences, Purdue University, West Lafayette, Indiana
| | - Uzay E Emir
- School of Health Sciences, Purdue University, West Lafayette, Indiana
| | - Ramon G Gonzalez
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stephan Gruber
- High Field MR Center, Department of Biomedical imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Rolf Gruetter
- Laboratory for Functional and Metabolic Imaging, Center for Biomedical Imaging, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Rakesh K Gupta
- Fortis Memorial Research Institute, Gurugram, Haryana, India
| | - Arend Heerschap
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anke Henning
- Max Planck Institute for Biological Cybernetics, Tuebingen, Germany
| | | | - Petra S Huppi
- Department of Pediatrics, University of Geneva, Geneva, Switzerland
| | - Ralph E Hurd
- Stanford Radiological Sciences Lab, Stanford, California
| | - Kejal Kantarci
- Department of Radiology, Mayo Clinic, Rochester, Minnesota
| | - Risto A Kauppinen
- School of Psychological Science, University of Bristol, Bristol, England
| | | | - Roland Kreis
- Departments of Radiology and Biomedical Research, University of Bern, Bern, Switzerland
| | | | - Martin O Leach
- CRUK Cancer Imaging Centre, Institute of Cancer Research and Royal Marsden Hospital, London, England
| | - Alexander P Lin
- Center for Clinical Spectroscopy, Brigham and Women's Hospital, Harvard University Medical School, Boston, Massachusetts
| | | | - Małgorzata Marjańska
- Department of Radiology, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota
| | | | - Dieter J Meyerhoff
- DVA Medical Center and Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | | | - Paul G Mullins
- Bangor Imaging Unit, School of Psychology, Bangor University, Bangor, Wales
| | | | - Sarah J Nelson
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | | | - Gülin Öz
- Department of Radiology, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota
| | - Julie W Pan
- Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Andrew C Peet
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, England
| | - Harish Poptani
- Centre for Preclinical Imaging, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Stefan Posse
- Department of Neurology, University of New Mexico, Albuquerque, New Mexico
| | - Eva-Maria Ratai
- Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nouha Salibi
- MR R&D, Siemens Healthineers, Malvern, Pennsylvania
| | - Tom W J Scheenen
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Brian J Soher
- Department of Radiology, Duke University Medical Center, Durham, North Carolina
| | - Ivan Tkáč
- Department of Radiology, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, Minnesota
| | - Daniel B Vigneron
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Franklyn A Howe
- Molecular and Clinical Sciences, St George's University of London, London, England
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Zhang Y, Liu X, Zhou J, Bottomley PA. Ultrafast compartmentalized relaxation time mapping with linear algebraic modeling. Magn Reson Med 2017; 79:286-297. [PMID: 28401643 DOI: 10.1002/mrm.26675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/17/2017] [Accepted: 02/19/2017] [Indexed: 12/28/2022]
Abstract
PURPOSE To dramatically accelerate compartmental-average longitudinal (T1 ) and transverse (T2 ) relaxation measurements using the minimal-acquisition linear algebraic modeling (SLAM) method, and to validate it in phantoms and humans. METHODS Relaxation times were imaged at 3 Tesla in phantoms, in the abdomens of six volunteers, and in six brain tumor patients using standard inversion recovery and multi-spin-echo sequences. k-space was fully sampled to provide reference T1 and T2 measurements, and SLAM was performed using a limited set of phase encodes from central k-space. Anatomical compartments were segmented on scout images post-acquisition, and SLAM reconstruction was implemented using two algorithms. Compartment-average T1 and T2 measurements were determined retroactively from fully sampled data sets, and proactively from SLAM data sets at acceleration factors of up to 16. Values were compared with reference measurements. The compartment's localization properties were analyzed using the discrete spatial response function. RESULTS At 16-fold acceleration, compartment-average SLAM T1 measurements agreed with the full k-space compartment-average results to within 0.0% ± 0.7%, 1.4% ± 3.4%, and 0.5% ± 2.9% for phantom, abdominal, and brain T1 measurements, respectively. The corresponding T2 measurements agreed within 0.2% ± 1.9%, 0.9% ± 7.9%, and 0.4% ± 5.8%, respectively. CONCLUSION SLAM can dramatically accelerate relaxation time measurements when compartmental or lesion-average values can suffice, or when standard relaxometry is precluded by scan-time limitations. Magn Reson Med 79:286-297, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Yi Zhang
- Division of MR Research, Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Xiaoyang Liu
- Division of MR Research, Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jinyuan Zhou
- Division of MR Research, Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA.,F. M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Paul A Bottomley
- Division of MR Research, Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA
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