Table 2.

Recommendations for preprocessing operations to remove/correct spectral imperfections.

Name of operation	Recommendation
Eddy current correction	- An eddy current correction should be applied routinely during the preprocessing of any in vivo MRS dataset. - For accurate eddy current estimation, the unsuppressed water scan must be collected from the same voxel location and using the exact same gradient scheme as the water suppressed data (e.g. turn only water suppression RF pulses off for unsuppressed water acquisition.) - Some analysis software packages (LCModel54, Tarquin61, FiTAID62) perform an eddy current correction at the analysis stage, obviating the need to perform this step in advance.
Motion correction	- For small amounts of motion, correct the resulting frequency and phase jitter using a frequency and phase drift correction (see below). - More severe bulk motion is indicated by individual transients that stand out as significantly different from the rest. Identify these “corrupted” transients either by visual inspection or by unsupervised outlier detection, and remove them prior to analysis. - If more than ~30% of the acquired transients are corrupted by motion, we recommend discarding that particular dataset since a) the likelihood of significant unwanted sampling of tissue outside the region of interest is high, and b) the continued removal of transients has a detrimental effect on the final SNR.
Frequency and phase drift correction	- Frequency and phase drift correction should be applied routinely for in vivo MRS, provided that there is enough SNR in the individual (or a few summed) transients to achieve robust frequency and phase estimation. - There are many effective methods for retrospective frequency and phase drift correction. We recommend methods that make use of the full spectrum (unless a weakly suppressed water peak is used for alignment). -Where available, the use of vendor-provided online drift corrections is recommended, provided that their performance has been well-validated; but offline retrospective drift correction is still recommended.
Alignment of subtraction sub-spectra	- Subtraction-based MRS techniques should always be coupled with an appropriate alignment procedure to align sub-spectra prior to subtraction. The choice of alignment procedure depends on the acquisition method. - In J-difference edited MRS, retrospective alignment of subtraction sub-spectra does not restore drift-induced reductions in editing efficiency.
Nuisance peak removal	- It is always preferable to remove nuisance signals at the level of the acquisition, rather than via preprocessing. - If necessary, large water and lipid signals can either be removed prior to analysis, or accounted for in the analysis model. Alternatively, one can adjust the frequency range over which spectral analysis is performed, in order to avoid nuisance signals. - Spurious echoes should be identified by visual inspection. - Since processing methods to remove spurious echoes are not widely available, we recommend that spectra contaminated by large spurious echoes should be discarded from further analysis, particularly if the spurious echoes are obscuring the metabolite peaks of interest.