Preprocessing, analysis and quantification in single‐voxel magnetic resonance spectroscopy: experts' consensus recommendations

Abstract

Once an MRS dataset has been acquired, several important steps must be taken to obtain the desired metabolite concentration measures. First, the data must be preprocessed to prepare them for analysis. Next, the intensity of the metabolite signal(s) of interest must be estimated. Finally, the measured metabolite signal intensities must be converted into scaled concentration units employing a quantitative reference signal to allow meaningful interpretation. In this paper, we review these three main steps in the post-acquisition workflow of a single-voxel MRS experiment (preprocessing, analysis and quantification) and provide recommendations for best practices at each step. Abbreviations: 1 H, proton; 13 C, carbon-13; B 0 , main magnetic field; B 1 , RF field; Cr, creatine; CRMVB, Cramér-Rao minimum variance bound; CSF, cerebrospinal fluid; d GM , water density of grey matter; d WM , water density of white matter; ERETIC, Electric Reference to Access in vivo Concentrations; f CSF , volume fraction of cerebrospinal fluid inside the MRS voxel; fCSF H2O , water mole fraction in cerebrospinal fluid; fGM, volume fraction of gray matter inside the MRS voxel; fGM H2O , water mole fraction in gray matter; FFT, fast Fourier transform; FID, free induction decay; FQN, fit quality number; FWHM, full width at half maximum; f WM , volume fraction of white matter inside the MRS voxel; fWM H2O , water mole fraction in white matter; GM, grey matter; GPC, glycerophosphocholine; [H 2 O] molal , water concentration in moles of water per kilogram of tissue water = 55.49 moles/kg; [H 2 O] molar , water concentration in moles of water per liter of tissue water; HERMES, Hadamard encoding and reconstruction of MEGA-edited spectroscopy; MEGA-PRESS, Mescher-Garwood point resolved spectroscopy; [M] GM /[M] WM , assumed ratio of grey matter to white matter metabolite concentrations; MM, macromolecules; [M]molal, metabolite concentration in moles of metabolite per kilogram of tissue water; [M]molar, metabolite concentration in moles of metabolite per liter of tissue water; MRSI, magnetic resonance spectroscopic imaging; NAA, N-acetylaspartate; NAAG, N-acetylaspartylglutamate; N M , number of protons contributing to metabolite signal; N P , number of points in FID/spectrum; N pc , number of phase encoding steps in one phase cycle; N RF , number of RF channels; N tra , number of transients;PCh, phosphocholine; PCr, phosphocreatine; RH2O CSF , relaxation scaling factor for water in cerebrospinal fluid; RH2O GM , relaxation scaling factor for water in grey matter; RH2O WM , relaxation scaling factor for water in white matter; RM, relaxation scaling factor for tissue metabolite signal; RM GM , relaxation scaling factor for metabolite in grey matter; RM WM , relaxation scaling factor for metabolite in white matter; S H2O , water signal intensity; SH2O obs , observed water signal intensity in the presence of relaxation; S M , metabolite signal intensity; SM obs , observed metabolite signal intensity in the presence of relaxation; SNR, signal-to-noise r...

In Vivo Molecular Signatures of Cerebellar Pathology in Spinocerebellar Ataxia Type 3

“…Localized 1 H‐MR spectra were acquired with a localization by adiabatic selective refocusing sequence (echo time = 15 milliseconds, repetition time = 5 seconds, 256 averages) 48 as described previously 44,45 . Spectra were saved as single scans, which were frequency and phase corrected 49 . Frequency drifts were corrected in the time domain after peak picking in frequency domain (the total creatine peak at 3 ppm) by using the first transient as reference.…”

“…Similarly, phase correction was done in the time domain by calculating the phase difference between the reference (first) transient and other transients. Transients that showed evidence for motion (substantial deviations in frequency, line width, signal‐to‐noise ratio, loss of water suppression efficiency relative to other transients) were excluded prior to averaging 49 . In the 23 spectra obtained from the Q84/Q84 cohort (mice that were included in the MRS analysis), 1 to 2 shots (of 256) were excluded in 3 spectra, 45 shots were excluded in 1 spectrum, and the acquisition had to be stopped because of gasping in 1 mouse, generating 110 usable shots.…”

Me, myself, bye: regional alterations in glutamate and the experience of ego dissolution with psilocybin

“…Spectra were acquired with the stimulated echo acquisition mode [51] sequence (TE = 6.0 ms, TR = 5.0 s, 64 averages). Outcome measures for MRS were concentration ratios of glutamate, GABA, NAA, and mI, to total Creatine (tCr, Creatine + Phospho-Creatine), because using tCr as the internal reference inherently corrects for variabilities caused by transmit or receive RF inhomogeneity, magnetic field drift, and CSF inclusion in the voxel [52].…”

Macromolecule suppressed GABA levels show no relationship with age in a pediatric sample

“…We report quantified MM-supp GABA in molal units, accounting for tissue specific relaxation and mole fractions of water as per standard MRS quantification approaches 23 . As secondary and follow-up analyses, we report MM-supp GABA including the "α-correction" 22 , which accounts for the higher concentration of GABA in grey matter (GM) compared to white matter (WM) (α = 0.5, which assumes the concentration of GABA in GM Statistical analysis.…”