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.
in GABA quantification ,we first select the file in the “SVS_EDIT_GABA_ACC_0011”
and second, we do the settings
third we select the the file in the “SVS_EDIT_GABA_ACC_0012”
I read the LCModel manual, in the book, it said that we have to use the “off-edit”, so we select the file in “SVS_EDIT_GABA_ACC_0012”
this is the files in the folder
three files in each folder.
prefessor, When performing Mega-Press analysis, I need to select files twice. Could you tell me if I also need to select files twice when analyzing in the “edit-off” mode? I guess it might be selecting the same file twice?
There are only three files in the folder, yes? If so, don’t select the folder as the input; select one of the .IMA files instead.
I don’t recall fully, but I believe of those three .IMA files is the GABA-edited difference (“DIFF”) spectrum. I think it’s the third one ending in *902.IMA. The “edit-OFF” file then should be the second one ending in *996.IMA.
The third one is the GABA-edited difference spectrum, but it is phased upside-down. There should be an option in the “Control Parameters” window to select: SPTYPE = 'mega-press-3'. That might fix the phasing.
