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Comparison of methods for spectral alignment and signal modelling of GABA-edited MR spectroscopy data

Reuben Rideaux, Mark Mikkelsen, Richard A. Edden
2021 NeuroImage  
Many methods exist for aligning and quantifying magnetic resonance spectroscopy (MRS) data໿ to measure in vivo γ-aminobutyric acid (GABA).  ...  and phase drift correction) and six GABA signal modelling methods.  ...  Acknowledgements We thank the Reviewers for their insightful comments and suggestions. The work was supported by the Leverhulme Trust ( ECF-2017-573 ), the Isaac Newton Trust ( 17.08(o) ).  ... 
doi:10.1016/j.neuroimage.2021.117900 pmid:33652146 fatcat:gvoooufmsre5rknbui77424xni

Importance of linear combination modeling for quantification of Glutathione and GABA levels using Hadamard-edited MRS [article]

Yulu Song, Helge J Zollner, Steve C.N. Hui, Georg Oeltzschner, James J Prisciandaro, Richard A.E. Edden
2021 bioRxiv   pre-print
Recent consensus recommended LCM as the method of choice for the spectral analysis of edited data.  ...  Purpose: Two main approaches are used for spectral analysis of edited data: simple peak fitting and linear combination modeling (LCM) with a simulated basis set.  ...  However, MR spectra require modeling to determine the size of signals, and in the common case of spectral overlap, to assign signal to particular metabolites.  ... 
doi:10.1101/2021.12.28.474256 fatcat:6oxhou5jkrayve427vqt4vejx4

INSPECTOR: free software for magnetic resonance spectroscopy data inspection, processing, simulation and analysis

Martin Gajdošík, Karl Landheer, Kelley M. Swanberg, Christoph Juchem
2021 Scientific Reports  
AbstractIn vivo magnetic resonance spectroscopy (MRS) is a powerful tool for biomedical research and clinical diagnostics, allowing for non-invasive measurement and analysis of small molecules from living  ...  Moreover, available MRS software focuses on selected aspects of MRS such as simulation, signal processing or analysis, necessitating the use of multiple packages and interfacing among them for biomedical  ...  The Data page contains methods for loading and saving protocol files, loading data, quality assessment (QA), and spectral alignment for averaging individual traces into a single spectrum used in further  ... 
doi:10.1038/s41598-021-81193-9 pmid:33483543 fatcat:vxhgbjmir5hk7isj276rks547m

Quantifying the effects of head movement on magnetic resonance spectroscopy estimates of gamma-aminobutyric acid [article]

Edward DongBo Cui, Richard J Maddock, Michael H Buonocore, Meric Ozturk, Jong H Yoon
2018 bioRxiv   pre-print
We conclude that head movement can significantly affect GABA measurements and the application of methods to account for movement may improve of GABA measurement accuracy and the detection of true group  ...  We developed a method to quantify and characterize head movement during GABA spectroscopy and found that two parameters of movement, displacement and instantaneous movement, were inversely correlated with  ...  Discussion We developed a method for quantifying in-scanner head movement and applied it to single voxel J-difference proton spectroscopy of neural GABA.  ... 
doi:10.1101/381699 fatcat:ttg2px2fwzbtzm5ocv2ea2bue4

Prospective frequency and motion correction for edited 1H magnetic resonance spectroscopy

Anouk Marsman, Anna Lind, Esben Thade Petersen, Mads Andersen, Vincent Oltman Boer
2021 NeuroImage  
HERMES spectral editing data showed to be more sensitive to motion, as significant differences in metabolite estimates and variability of spectral quality measures were observed for tCr, GABA+ and GSH  ...  Conventional MRS is acquired at relatively short echo times (TE), however, for unambiguous detection of GABA and GSH, spectral editing techniques are typically used.  ...  For edited HERMES spectra, frequency alignment, phasing and artifact detection was performed for each of the four steps separately before a final step that performed phase and frequency alignment on the  ... 
doi:10.1016/j.neuroimage.2021.117922 pmid:33662573 fatcat:leqhjef5dnbtbcawdxnou36a7y

Dual-volume excitation and parallel reconstruction for J-difference-edited MR spectroscopy

Georg Oeltzschner, Nicolaas A.J. Puts, Kimberly L. Chan, Vincent O. Boer, Peter B. Barker, Richard A.E. Edden
2016 Magnetic Resonance in Medicine  
Purpose-To develop J-difference editing with Parallel Reconstruction in Accelerated Multivoxel (PRIAM) for simultaneous measurement of γ-aminobutyric acid (GABA) and glutathione in two separate brain regions  ...  Methods-PRIAM separates signals from two simultaneously excited voxels using receiver-coil sensitivity profiles.  ...  GABA spectra were aligned using Spectral Registration (21) .  ... 
doi:10.1002/mrm.26536 pmid:27851878 pmcid:PMC5422131 fatcat:5mlrtbtddzb2hlitlrzs6z3rqu

Osprey: Open-Source Processing, Reconstruction & Estimation of Magnetic Resonance Spectroscopy Data [article]

Georg Oeltzschner, Helge J. Zoellner, Steve C. N. Hui, Mark Mikkelsen, Muhammad G. Saleh, Sofie Tapper, Richard A. E. Edden
2020 bioRxiv   pre-print
Results: Osprey successfully loads, processes, models, and quantifies MRS data acquired with a variety of conventional and spectral editing techniques.  ...  New Method: Osprey loads multiple common MRS data formats, performs phased-array coil combination, frequency-and phase-correction of individual transients, signal averaging and Fourier transformation.  ...  Acknowledgements This work was supported by NIH grants K99AG062230, R21AG060245, R01EB016089, R01EB023963, and P41EB015909. None of the authors have a competing interest to declare.  ... 
doi:10.1101/2020.02.12.944207 fatcat:cb6wekhlyfetfh3a5sz24dohta

A comparison of sLASER and MEGA-sLASER using simultaneous interleaved acquisition for measuring GABA in the human brain at 7T

Donghyun Hong, Seyedmorteza Rohani Rankouhi, Jan-Willem Thielen, Jack J. A. van Asten, David G. Norris, Peter Lundberg
2019 PLoS ONE  
Currently, the prevalent methods for detecting GABA at ultrahigh field strengths (≥ 7 T) are GABA-editing and model fitting of non-editing single voxel spectra.  ...  This simultaneous interleaved acquisition minimizes the differential effect of extraneous factors, and enables an accurate comparison of the two acquisition methods.  ...  Acknowledgments This work was funded by the Helmholtz Alliance ICEMED-Imaging and Curing Environmental Metabolic Diseases, through the Initiative and Networking Fund of the Helmholtz Association.  ... 
doi:10.1371/journal.pone.0223702 pmid:31603925 pmcid:PMC6788718 fatcat:x2uhdilk7ffhlhdkztxcmnbop4

Automatic frequency and phase alignment of in vivo J-difference-edited MR spectra by frequency domain correlation

Evita C. Wiegers, Bart W. J. Philips, Arend Heerschap, Marinette van der Graaf
2017 Magnetic Resonance Materials in Physics, Biology and Medicine  
Norris and co-workers (Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging, Radboud University Nijmegen) for supplying the J-difference-edited GABA spectra.  ...  B.E. de Galan (Department of Internal Medicine, Radboud university medical center) for their assistance during data acquisition. We are indebted to Dr. A.J.  ...  MRS protocol for the J-difference editing of GABA In addition, we applied the correlation method to J-difference-edited spectra of GABA optimized for detection of the GABA signal at 3.0 ppm.  ... 
doi:10.1007/s10334-017-0627-y pmid:28573461 pmcid:PMC5701960 fatcat:jedlyutbbrds7flble6axejv7i

Benchmarking GABA Quantification: A Ground Truth Data Set and Comparative Analysis of TARQUIN, LCModel, jMRUI and Gannet [article]

C. Jenkins and M. Chandler and F. C. Langbein and S. M. Shermer
2021 arXiv   pre-print
Many tools exist for the quantification of GABA-edited magnetic resonance spectroscopy (MRS) data.  ...  methods.  ...  The most common method for non-invasive detection of GABA in-vivo is magnetic resonance spectroscopy (MRS).  ... 
arXiv:1909.02163v2 fatcat:bv7o7s65wfbtldodlv2kqch5i4

Big GABA: Edited MR spectroscopy at 24 research sites

Mark Mikkelsen, Peter B. Barker, Pallab K. Bhattacharyya, Maiken K. Brix, Pieter F. Buur, Kim M. Cecil, Kimberly L. Chan, David Y.-T. Chen, Alexander R. Craven, Koen Cuypers, Michael Dacko, Niall W. Duncan (+48 others)
2017 NeuroImage  
Magnetic resonance spectroscopy (MRS) is the only biomedical imaging method that can noninvasively detect endogenous signals from the neurotransmitter γ-aminobutyric acid (GABA) in the human brain.  ...  Nevertheless, implementations of GABA-edited MRS remain diverse across research sites, making comparisons between studies challenging.  ...  Data collection was supported by the Shandong Provincial Key Research and Development Plan of China (2016ZDJS07A16) and the  ... 
doi:10.1016/j.neuroimage.2017.07.021 pmid:28716717 pmcid:PMC5700835 fatcat:t5ernqj6s5cdfhq2twugxt5jjm

Comparison of seven modelling algorithms for GABA‐edited 1 H‐MRS

Alexander R. Craven, Pallab K. Bhattacharyya, William T. Clarke, Ulrike Dydak, Richard A. E. Edden, Lars Ersland, Pravat K. Mandal, Mark Mikkelsen, James B. Murdoch, Jamie Near, Reuben Rideaux, Deepika Shukla (+5 others)
2022 NMR in Biomedicine  
Edited MRS sequences are widely used for studying GABA in the human brain.  ...  GABA-edited (GABA+, TE = 68 ms MEGA-PRESS) data from 222 subjects at 20 sites were processed via a standardised pipeline, before modelling with FSL-MRS, Gannet, AMARES, QUEST, LCModel, Osprey and Tarquin  ...  | INTRODUCTION Several software packages and modelling algorithms are available for processing and quantifying MR spectroscopy (MRS) data.  ... 
doi:10.1002/nbm.4702 pmid:35078266 pmcid:PMC9203918 fatcat:paik7nzjjbh3ve5spmvk6boyjq

Advanced Hadamard-encoded editing of seven low-concentration brain metabolites: Principles of HERCULES

Georg Oeltzschner, Muhammad G. Saleh, Daniel Rimbault, Mark Mikkelsen, Kimberly L. Chan, Nicolaas A.J. Puts, Richard A.E. Edden
2019 NeuroImage  
To demonstrate the framework of a novel Hadamard-encoded spectral editing approach for simultaneously detecting multiple low-concentration brain metabolites in vivo at 3T.  ...  Acknowledgements The authors would like to express their gratitude to David Lythgoe and Diana Rotaru (King's College, United Kingdom) for sharing their FID-A implementation of the fast spatial simulation  ...  This work was supported by NIH grants R01 EB016089, R01 EB023963, U54 HD079123, and P41 EB015909. NAJP receives support from NIH grant K99/R00 MH107719.  ... 
doi:10.1016/j.neuroimage.2018.10.002 pmid:30296560 pmcid:PMC6289748 fatcat:w7k2em3h3nbfhatnyyj2twzj6a

On the reproducibility of hippocampal MEGA-sLASER GABA MRS at 7T using an optimized analysis pipeline

Yannik Völzke, Eberhard D. Pracht, Elke Hattingen, Desmond H. Y.Tse, Tony Stöcker
2020 Magnetic Resonance Materials in Physics, Biology and Medicine  
The increased spectral dispersion of ultra-high-field spectroscopy allows for reproducible spectral quantification, despite a very broad line width.  ...  However, the low concentration and the overlap of more prominent resonances hamper GABA quantification using MR spectroscopy. The hippocampus plays a pivotal role in neurodegeneration.  ...  However, GABA-MRS is hampered by its inherently low signal and the overlap of more prominent resonances. J-difference editing is often used to remove these overlapping resonances [5] .  ... 
doi:10.1007/s10334-020-00879-9 pmid:32865653 pmcid:PMC8154804 fatcat:62iphwbi6rhololh5ae4dwn5t4

MRSNet: Metabolite Quantification from Edited Magnetic Resonance Spectra With Convolutional Neural Networks [article]

M. Chandler, C. Jenkins, S. M. Shermer, F. C. Langbein
2019 arXiv   pre-print
A large range of network structures, data representations and automatic processing methods are investigated.  ...  For example, the neurotransmitter γ-aminobutyric acid (GABA), present in very low concentration in vivo, regulates inhibitory neurotransmission in the brain and is involved in several processes outside  ...  MC would like to thank EPSRC and Cardiff University for doctoral funding.  ... 
arXiv:1909.03836v1 fatcat:j7qdtpmowjdhbn3q65veygcqpq
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