Supplementary Methods: 1H-MRS data acquisition and analysis
1H-MRS acquisition
1H-MRS spectra were acquired on a General Electric (Milwaukee, Wisconsin, USA) 3
Tesla HDx MR system. As detailed previously,1, 2 subjects underwent an initial
localizer scan followed by acquisition of structural images including an axial 2D T2weighted fast spin echo scan and an axial fast fluid-attenuated inversion recovery
scan (total scan time = 5 min). These were followed by a whole-brain threedimensional coronal inversion recovery prepared spoiled gradient echo (IR-SPGR)
scan, giving isotropic 1.1-mm voxels in a scan time of approximately 6 min (echo
time (TE) = 2.82 msec; repetition time (TR) = 6.96 msec; inversion time = 450 msec;
excitation flip angle = 20°).
1H-MRS
spectra (PRESS—Point RESolved Spectroscopy; TE = 30 msec; TR = 3000
msec; 96 averages) were acquired using the standard GE PROBE (PROton Brain
Examination) sequence, which uses a standardized CHEemical Shift Selective (CHESS)
water suppression routine, as previously described.1, 2 For each metabolite
spectrum, unsuppressed water reference spectra (16 averages) were also collected
as part of the acquisition. Shimming was optimized, with auto-prescan performed
twice before each scan. Using standardized protocols, voxels were prescribed in the
left thalamus (15 x 20 x 20 mm right–left, anterior–posterior, superior–inferior) and
anterior cingulate cortex (ACC, 20 x 20 x 20 mm). The left thalamic voxel was
positioned to include the maximum amount of grey matter based on individual
anatomy. The ACC voxel was prescribed from the midline sagittal localizer, with the
center of the voxel placed 13 mm above the genu of corpus callosum perpendicular
to the AC–PC line.
1H-MRS
quantification
For compatibility with our previous report1 spectra were analyzed using LCModel
version 6.1-4 F3, using a standard basis set of 16 metabolites (L-alanine, aspartate,
creatine, phosphocreatine, ϒ-amino butyric acid (GABA), glucose, glutamine,
glutamate, glycerophosphocholine, glycine, myo-inositol, L-lactate, Nacetylaspartate (NAA), N-acetylaspartylglutamate, phosphocholine, and taurine),
acquired with the same field strength (3 Tesla), localization sequence (PRESS) and
echo time (30 msec). Model metabolites and concentrations used in the basis set are
fully detailed in the LCModel manual (http://s-provencher-.com/pages/lcmmanual.shtml). Poorly fitted metabolite peaks (Cramer–Rao minimum variance
bounds (CRLB) of >20% as reported by LCModel) were excluded from further
analysis. NAA is reported in combination with N-acetylaspartylglutamine (NAAG). For
all metabolites present in the 1H-MRS spectra, quantitative concentrations were
calculated in units of mmol, but to indicate that these values have not been scaled to
allow for the effects of T1 or T2 relaxation, results are presented as ‘institutional
units’.
The IR-SPGR scans were used for localization of the spectroscopy voxels and were
segmented into grey matter, white matter and cerebrospinal fluid (CSF) using
Statistical Parametric Mapping 2 software (SPM2; Wellcome Trust Centre for
Neuroimaging, Institute of Neurology, University College London, United Kingdom)
to allow correction of water-scaled 1H-MRS metabolite values for partial volume CSF
contamination. Metabolite values were corrected for the presence of CSF in the
voxel using the formula Mcorr = M/(wm +gm), where M is the uncorrected
metabolite value, and wm and gm are the white and grey matter fractions from the
segmented images (ranging between 0 and 1) for the spectroscopy voxel. Since the
metabolite measures were derived with water-scaling, a further correction was
applied to correct the estimated water concentration of the voxel for partial volume
CSF contamination, assuming a CSF water concentration of 55,556 mol/m3 and the
LCModel default brain water concentration of 35,880 mol/m3 (http://s-provencher.com/pages/lcm-manual.shtml). For practical purposes, these two correction factors
were combined into a single equation which simplifies to Mcorr = M*(wm+gm +
1.55CSF) / (wm+gm), where CSF is the fraction of the voxel filled with cerebrospinal
fluid.
1.
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