Dear Gannet team,
I’m an undergraduate researcher who’s been assigned a study that involves Gannet. I’ve spent the past couple of days familiarizing myself with the software, and I’ve got it mostly running. I just had a couple of questions.
When I run GannetQuantify, is there any way to include GSH/Cr in the figure? I’ve managed to get a concentration through the command window using “MRS_struct.out.vox1.GSH.ConcCr” and changing the acquisition parameters to GSH instead of GABAGlx, but I would really appreciate being able to skip that step in the command window and instead implement it in files.
Moreover, I was wondering whether it is possible to obtain measurements of GSH and GABAGlx from a single command? I know it’s usually advised not to use AI for this sort of thing, since it can make a ton of mistakes, but they suggested I incorporate it.
“MRS_struct.p.target = {‘GSH’};
MRS_struct.p.target2 = {‘GABAGlx’};”
into GannetPreInitialise to get it going. However, as I expected, I keep getting error messages. If anyone has any suggestions, I would greatly appreciate it.
Thank you & have a great day!
Hi @JosephBorna,
It’s great to hear that you’ve been using Gannet.
Could you share a bit more detail about your data? For example, did you acquire GABA-edited data using a standard MEGA-PRESS sequence? If so, it won’t be possible to quantify GSH. This is because GABA-edited MRS acquisitions are optimized to unambiguously resolve the GABA signal (and some other metabolite signals), but not GSH.
If you can provide more information about your MRS acquisition, I can confirm what is and isn’t possible in Gannet given your data.
Mark
Thank you for your reply, and I apologize for the delayed response.
I’ve been looking through the protocols, and it seems like I am using GABA-edited data acquired with a standard MEGA-PRESS sequence (svs_ed) at TE = 68 ms on a 3T Siemens scanner, with ON and OFF subspectra. Sorry, I’m still pretty new to MRS.
I ran through about 80 patients, and for about 15, negative concentrations were returned. I tried implementing some suggestions from the “-GABA” page, but still no luck, even after changing my target to GABAGlx (in fact, more concentrations were becoming negative). Is there anything else you recommend?
Thank you,
Joseph
Thanks for checking. So, you will not be able to quantify GSH from these data; only GABA and Glx.
Could you please share some example GannetLoad and GannetFit PDFs? Especially when there is a negative concentration estimate?
Also, are you using the latest version of Gannet? From the syntax you provided, I suspect that you are using an outdated version.
Mark