Good morning, distinguished experts. I am currently using LCModel for GABA quantification. My output results include NAA, so I am defaulting to NAA as the reference (ref). I would like to consult you on the following questions:
Why is there no Creatine (Cr) in my output results?
Is the absence of Cr results caused by the basis set used?
Could the absence of Cr be due to my scanning parameters? Since my TE (Echo Time) is 68ms.
I have seen in some articles that Creatine is used as the reference (i.e., GABA/Cr ratio), but my results only show the GABA/NAA ratio. Will this lead to questions or doubts from others?
I have heard that NAA is generally used as the reference for GABA quantification. Is there such a common practice or statement?
If you don’t provide LCModel with an unsuppressed water signal to perform absolute quantification, it will quantify GABA relative to total NAA (NAA+NAAG) because the Cr signal is subtracted out in the GABA-edited spectrum. More details are provided in sections 9.4 and 9.4.2 the LCModel manual (attached below).
You could input the edit-OFF spectrum of your (I assume) MEGA-PRESS data to fit the Cr signal to derive GABA/tCr, but you would need an appropriate basis set for such a spectrum. You could use a short-TE PRESS spectrum, but you would need to correct the scaling (see section 9.4.1.3 in the manual).
While not as common as Cr-referencing, NAA-referencing is just as valid and comes with the same assumptions (e.g., NAA is not systematically different between groups).
Thank you professor
I will study the manual.
1.Our scans include both OFF and ON states, but our basis set does not contain Cr (creatine). Could this lead to the absence of Cr data? And if i do not have the basis. i could not get the Cr?
2.Additionally, you mentioned using a short TE (echo time). Since all our scans have already been completed, is it no longer possible to do this?
3.I have read several papers about NAA as reference and its TE = 68ms.Do you have a recommand paper about NAA as ref(with high IF).
Thank you, Professor.
Since you are modeling the difference spectrum (ON – OFF), there is no Cr in spectrum and therefore no Cr in the basis set. If you fit the OFF spectrum, you would need to have a different basis set that includes Cr.
Correct. Acquiring new short-TE data in the same participants would be problematic because it would be a new scan under new conditions (with biological, scanner-related, etc. differences).
I don’t have a single reference to recommend, but I would suggest reading this consensus paper, which discusses quantification using internal metabolite and tissue water references.