Quantification with short TE acquisition

Hi all, this might be a stupid question, but - what’s the “best practice” for acquiring MRS data and water data for “quantification”, when using short TE acquisition? Is simple unsuppresed water at the same TE sufficient?

I wouldn’t say there is a “best practice” per se. However, acquiring water data at short TE is beneficial because it lessens T2 weighting on the water signal and thus attenuates propagated errors in the T2 correction that must be applied to derive (pseudo-)absolute concentrations.

You would also want to acquire an additional water scan for eddy-current correction acquired using the same scan parameters as your metabolite water-suppressed acquisition, just without the water-suppression pulses.

Thanks. In case the actual spectra is acquired at short TE, the one (short TE) unsuppressed water would be used for both eddy-current correction and “quantification”, correct? And taking a turn to analysis, would I load this as “H2O reference” or “H2O short TE” if I were to use Osprey as an example?

Hi Peter,

On the Osprey question: The H2O reference (loaded as files_ref) is used for eddy current correction and requires same TE etc. as the water-suppressed scan, “H2O Short TE” (loaded as files_w) is used when you acquire a second water-unsuppressed scan at shorter TE to avoid the T2 weighting that Mark alluded to.

If—as seems to be the case for you—you acquire just a single water reference at a short TE that matches the water-suppressed scan, then you can just use the first option (files_ref). Osprey will use files_w for metabolite-water amplitudes if it exists, otherwise it will use files_ref.

Hope that helps,


Thanks Chris! Much appreciated

1 Like