Processing Phantom data

We have collected MRS data with PRESS sequence with a phantom only containing sodium acetate and lactic acid lithium salt like this:
But we are now confusing about how to process data from such phatom as there are no Cr or NAA peaks which are always used for alignment and preliminary fitting. So I wonder how can we process this data? Can we use the acetate peak as reference for correction and alignment? And which method are more suitbale for fitting data without Cr or NAA?

Hi @NSniper,

That depends a bit on what you’re hoping to do with the data after processing?

In principle, any stable, well-defined peak could be used for the referencing and alignment. In this case, acetate and residual water would be candidates; often (but not always) the metabolite signal is the better choice. Keep in mind that these will be shifted a bit relative to in-vivo temperatures.

Most software should give you some flexibility as to the choice of reference. The LCModel user manual has some useful suggestions, including in sections 11.3 “Prior Referencing Information” and 11.6, “Unusual Phantoms”. These should cover your situation pretty well.

For FSL-MRS, you could look at the --internal_ref option; maybe also --wref_metabolite, --ref_protons etc.

In terms of fitting approach: beware of overfitting – you should probably use a very restricted set of prior knowledge. Simple peak-fitting would probably be a good choice – perhaps with more “interactive” tools, such as jMRUI AMARES or whatever software is available on your scanner console.

Hi @alex ,
Thank you for the reply, that’s really helpful.