Noise suppression of proton magnetic resonance spectroscopy improves paediatric brain tumour classification.

machine learning metabolite concentration noise suppression paediatric brain tumour proton magnetic resonance spectroscopy wavelet

Journal

NMR in biomedicine
ISSN: 1099-1492
Titre abrégé: NMR Biomed
Pays: England
ID NLM: 8915233

Informations de publication

Date de publication:
17 Mar 2024
Historique:
revised: 07 01 2024
received: 12 04 2023
accepted: 03 02 2024
medline: 18 3 2024
pubmed: 18 3 2024
entrez: 17 3 2024
Statut: aheadofprint

Résumé

Proton magnetic resonance spectroscopy (

Identifiants

pubmed: 38494431
doi: 10.1002/nbm.5129
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

e5129

Subventions

Organisme : Health Data Research UK
Organisme : CHILDREN with CANCER UK
Organisme : Action Medical Research and the Brain Tumour Charity
Organisme : Birmingham Women's and Children's Hospital Charities
Organisme : The Children's Cancer and Leukaemia Group Little Princess Trust
Organisme : Cancer Research UK and NIHR Experimental Cancer Medicine Centre Paediatric Network
Organisme : Children's Research Fund
Organisme : NIHR Nottingham Biomedical Research Centre
Organisme : Cancer Research UK and EPSRC Cancer Imaging Programme at the Children's Cancer and Leukaemia Group (CCLG) in association with the MRC and Department of Health (England)
Organisme : NIHR Research Professorship
Organisme : Help Harry Help Others

Informations de copyright

© 2024 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.

Références

Aldape K, Brindle KM, Chesler L, et al. Challenges to curing primary brain tumours. Nat Rev Clin Oncol. 2019;16(8):509-520.
Steliarova-Foucher E, Colombet M, Ries LAG, et al. International incidence of childhood cancer, 2001-10: a population-based registry study. Lancet Oncol. 2017;18(6):719-731.
Rickert CH, Paulus W. Epidemiology of central nervous system tumors in childhood and adolescence based on the new who classification. Child's Nerv Syst. 2001;17(9):503-511.
Collins VP, Jones DT, Giannini C. Pilocytic astrocytoma: pathology, molecular mechanisms and markers. Acta Neuropathol. 2015;129(6):775-788.
Northcott PA, Robinson GW, Kratz CP, et al. Medulloblastoma. Nat Rev Dis Primers. 2019;5(1-20):11.
Kilday JP, Rahman R, Dyer S, et al. Pediatric ependymoma: Biological perspectives. Mol Cancer Res. 2009;7(6):765-786.
Louis DN, Perry A, Reifenberger G, et al. The 2016 world health organization classification of tumors of the central nervous system: A summary. Acta Neuropathol. 2016;131(6):803-820.
Pollack IF, Jakacki RI. Childhood brain tumors: epidemiology, current management and future directions. Nat Rev Neurol. 2011;7(9):495-506.
Parsons MW, Whipple NS, Poppe MM, Mendez JS, Cannon DM, Burt LM. The use and efficacy of chemotherapy and radiotherapy in children and adults with pilocytic astrocytoma. J Neurooncol. 2021;151(2):93-101.
Dressler EV, Dolecek TA, Liu M, Villano JL. Demographics, patterns of care, and survival in pediatric medulloblastoma. J Neurooncol. 2017;132(3):497-506.
Swanson EL, Amdur RJ, Morris CG, et al. Intracranial ependymomas treated with radiotherapy: long-term results from a single institution. J Neurooncol. 2011;102(3):451-457.
Wilne SH, Dineen RA, Dommett RM, Chu TP, Walker DA. Identifying brain tumours in children and young adults. BMJ. 2013;347:f5844.
Manias KA, Gill SK, MacPherson L, Foster K, Oates A, Peet AC. Magnetic resonance imaging based functional imaging in paediatric oncology. Eur J Cancer. 2017;72:251-265.
Regis J, Bouillot P, Rouby-Volot F, Figarella-Branger D, Dufour H, Peragut JC. Pineal region tumors and the role of stereotactic biopsy: Review of the mortality, morbidity, and diagnostic rates in 370 cases. Neurosurg. 1996;39(5):907-914.
Orphanidou-Vlachou E, Vlachos N, Davies NP, Arvanitis TN, Grundy RG, Peet AC. Texture analysis of t1- and t2-weighted mr images and use of probabilistic neural network to discriminate posterior fossa tumours in children. NMR Biomed. 2014;27(6):632-639.
Jeener J, Meier BH, Bachmann P, Ernst RR. Investigation of exchange processes by two-dimensional nmr spectroscopy. J Chem Phys. 1979;71(11):4546-4553.
Barker PB, Lin DDM. In vivo proton mr spectroscopy of the human brain. Prog Nucl Magn Reson Spectrosc. 2006;49(2):99-128.
Faubert B, Solmonson A, DeBerardinis RJ. Metabolic reprogramming and cancer progression. Science. 2020;368(6487):eaaw5473.
Haddadin IS, McIntosh A, Meisamy S, et al. Metabolite quantification and high-field mrs in breast cancer. NMR Biomed. 2009;22(1):65-76.
Preul MC, Caramanos Z, Collins DL, et al. Accurate, noninvasive diagnosis of human brain tumors by using proton magnetic resonance spectroscopy. Nat Med. 1996;2(3):323-325.
Keevil SF. Spatial localization in nuclear magnetic resonance spectroscopy. Phys Med Biol. 2006;51(16):R579-636.
Levitt MH. Fourier transform nmr. In: Levitt MH, ed. Spin dynamics. Second Edition. Chichester, West Sussex, England: John Wiley & Sons Ltd; 2007:86.
Kreis R. Issues of spectral quality in clinical 1h-magnetic resonance spectroscopy and a gallery of artifacts. NMR Biomed. 2004;17(6):361-381.
Kreis R, Boer V, Choi IY, et al. Terminology and concepts for the characterization of in vivo MR spectroscopy methods and MR spectra: Background and experts' consensus recommendations. NMR Biomed. 2020;34(5):e4347.
Wilson M, Andronesi O, Barker PB, et al. Methodological consensus on clinical proton mrs of the brain: Review and recommendations. Magn Reson Med. 2019;82(2):527-550.
Rioul O, Vetterli M. Wavelets and signal processing. IEEE Signal Process Mag. 1991;8(4):14-38.
Serrai H, Senhadji L, Jacques D, Coatrieux JL. Time-domain quantification of amplitude, chemical shift, apparent relaxation time t*2, and phase by wavelet-transform analysis: Application to biomedical magnetic resonance spectroscopy. J Magn Reson. 1997;124(1):20-34.
Antoine JP, Chauvin C, Coron A. Wavelets and related time-frequency techniques in magnetic resonance spectroscopy. NMR Biomed. 2001;14(4):265-270.
Cancino-De-Greiff HF, Ramos-Garcia R, Lorenzo-Ginori JV. Signal de-noising in magnetic resonance spectroscopy using wavelet transforms. Concepts Magn Reson. 2002;14(6):388-401.
Stanwell P, Siddall P, Keshava N, et al. Neuro magnetic resonance spectroscopy using wavelet decomposition and statistical testing identifies biochemical changes in people with spinal cord injury and pain. Neuroimage. 2010;53(2):544-552.
Wilson M, Reynolds G, Kauppinen RA, Arvanitis TN, Peet AC. A constrained least-squares approach to the automated quantitation of in vivo 1H magnetic resonance spectroscopy data. Magn Reson Med. 2011;65(1):1-12.
Cavassila S, Deval S, Huegen C, van Ormondt D, Graveron-Demilly D. Cramér-Rao bounds: an evaluation tool for quantitation. NMR Biomed. 2001;14(4):278-283.
Zhao D, Grist JT, Sun Y, Peet AC. Impact of wavelets and apodisation in magnetic resonance spectroscopy quality for paediatric brain tumours. Proc Intl Soc Magn Reson Med. 2019;27:4243.
Hand DJ, Till RJ. A simple generalisation of the area under the ROC curve for multiple class classification problems. Mach Learn. 2001;45(2):171-186.
Zhao D, Grist JT, Rose HEL, et al. Metabolite selection for machine learning in childhood brain tumour classification. NMR Biomed. 2022;35(6):e4673.
Chawla NV, Bowyer KW, Hall LO, Kegelmeyer WP. SMOTE: Synthetic minority over-sampling technique. J Artif Intell Res. 2002;16:321-357.
Quinlan JR. Induction of decision trees. Mach Learn. 1986;1:81-106.
Robin X, Turck N, Hainard A, et al. pROC: An open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinform. 2011;12:77.
Stéphane M. Denoising. In: Stéphane M, ed. A wavelet tour of signal processing, the sparse way. Third Edition. Boston: Academic Press; 2009:535-610.
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 Biomed. 2021;34(6):e4497.
Cramér H. A contribution to the theory of statistical estimation. Scand Actuar J. 1946;1946(1):85-94.
Near J, Harris AD, Juchem C, et al. Preprocessing, analysis and quantification in single-voxel magnetic resonance spectroscopy: Experts' consensus recommendations. NMR Biomed. 2021;34(5):e4257.
Clarke WT, Chiew M. Uncertainty in denoising of MRSI using low-rank methods. Magn Reson Med. 2022;87(2):574-588.
Arora RS, Alston RD, Eden TO, Estlin EJ, Moran A, Birch JM. Age-incidence patterns of primary cns tumors in children, adolescents, and adults in england. Neuro Oncol. 2009;11(4):403-413.
Sullivan LB, Gui DY, Heiden MGV. Altered metabolite levels in cancer: Implications for tumour biology and cancer therapy. Nat Rev Cancer. 2016;16(11):680-693.
Arts LPA, van den Broek EL. The fast continuous wavelet transformation (fcwt) for real-time, high-quality, noise-resistant time-frequency analysis. Nat Comput Sci. 2022;2(1):47-58.

Auteurs

Teddy Zhao (T)

Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
Oncology, Birmingham Children's Hospital, Birmingham, UK.

James T Grist (JT)

Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.

Dorothee P Auer (DP)

Clinical Neuroscience, University of Nottingham, Nottingham, UK.

Shivaram Avula (S)

Radiology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK.

Simon Bailey (S)

Paediatric Oncology, Great North Children's Hospital, Newcastle upon Tyne, UK.

Nigel P Davies (NP)

Imaging and Medical Physics, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.

Richard G Grundy (RG)

Clinical Neuroscience, University of Nottingham, Nottingham, UK.

Omar Khan (O)

Digital Healthcare, WMG, University of Warwick, Coventry, UK.

Lesley MacPherson (L)

Radiology, Birmingham Children's Hospital, Birmingham, UK.

Paul S Morgan (PS)

Clinical Neuroscience, University of Nottingham, Nottingham, UK.
Children's Brain Tumour Research Centre, University of Nottingham, Nottingham, UK.
Medical Physics, Nottingham University Hospitals NHS Trust, Nottingham, UK.

Barry Pizer (B)

University of Liverpool, Liverpool, UK.

Heather E L Rose (HEL)

Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
Oncology, Birmingham Children's Hospital, Birmingham, UK.

Yu Sun (Y)

Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
Oncology, Birmingham Children's Hospital, Birmingham, UK.

Martin Wilson (M)

Centre for Human Brain Health, University of Birmingham, Birmingham, UK.

Lara Worthington (L)

Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
Oncology, Birmingham Children's Hospital, Birmingham, UK.
RRPPS, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.

Theodoros N Arvanitis (TN)

Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
Oncology, Birmingham Children's Hospital, Birmingham, UK.
Digital Healthcare, WMG, University of Warwick, Coventry, UK.
Engineering, University of Birmingham, Birmingham, UK.

Andrew C Peet (AC)

Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
Oncology, Birmingham Children's Hospital, Birmingham, UK.

Classifications MeSH