Hello, I am new to processing MRS data and Osprey but found the tool very easy to use and really appreciate all of the work on it!

I recently pushed a dataset through Osprey and am interested in GABA quantification. I know from the HERMES methods paper that to quantify GABA I should take the differences between the sum of the spectra with GABA “ON” and the sum of the spectra with GABA “OFF”. There are three outputs from quantification that are called “diff1”, “diff2”, and “sum”. I was wondering which of these to use? Any help is appreciated.

Also as a side note, even though I set my sequence to HERMES in my configuration file, I still see “HERCULES” at the top of the GUI for the sequence type. I am not sure why.

Hi @Claar727,

Nice to have you here, thanks for reaching out.

diff1 is the GABA-edited spectrum. You will need to calculate GABA+, i.e., the combined amplitude from GABA and the co-edited macromolecular signal (this will depend on the co-edited MM parametrization method that you have used in the job file).

(Not sure why it says HERCULES. Can you confirm that it is called HERMES and not HERCULES in your exam card?)


Thanks for your quick reply!

So I would add the GABA column in the tsv output from quantify step to the other MM columns to get the GABA+ concentration?

And I just checked our card and it has the sequence labeled as “HERMES_GABA_GSH_EtOH” and whenever I look at the header of the twix data using the twixtools package I see the name of the sequence is svs_hermes so I’m not sure why HERCULES would come up.

Not to all the other MM columns. You need to identify the MM basis function that contributes to the 3-ppm co-edited signal in the GABA-edited difference spectrum.

About the sequence name - which software version are you using and what exam card settings? You’re measuring ethanol then?