Dear Osprey/MRS experts,
I am currently designing/piloting an MRS study using the Johns Hopkins MEGA-PRESS sequence (metabolite of interest is GABA). I plan to use Osprey to analyse my data but am running into issues during analysis that I suspect are due to my acquisition parameters.
Oeltzschner et al.'s 2020 paper (doi: 10.1016/j.jneumeth.2020.108827), as well as the Osprey jobfile and manual suggest that three files should (or can) be used in the analysis: the metabolite file (in my case using a MEGA-PRESS acquisition); lineshape reference data (acquired with the same sequence as the metabolite data, but without water suppression, and used to perform eddy-current correction); and short-TE reference data.
We are using a Siemens Prisma 3T scanner. When we attempted to acquire the lineshape reference data (water unsuppressed data), our scanner automatically changed the delta value to one that did not match the original MEGA-PRESS acquisition parameters. Should I leave this or adjust to match the original (water suppressed) sequence?
Secondly, I would like to know the recommended number of volumes for the lineshape reference and short TE reference scans. In my initial attempt, I tried collecting a single volume, which I was told would be sufficient but I suspect that this is contributing to the errors I am getting during analysis in Osprey. Should I perhaps be collecting 8 or even 16 volumes for these data?
Lastly, I wondered if anyone who has successfully acquired and analysed MEGA-PRESS data (using the TWIX files) in Osprey would mind sharing their sequence information please? This would make it much easier to see where we have gone wrong.
I attach my Osprey jobfile but as mentioned, I think the issues stem from the data rather than the program.osprey_jobfile.docx (18.6 KB)
On loading the data into Osprey, I get the error message:
Error using cat
Dimensions of arrays being concatenated are not consistent.
Error in io_loadspec_twix (line 401)
fids = cat(4,fids_A,fids_B,fids_C,fids_D);
Error in osp_LoadTwix (line 71)
raw_ref = io_loadspec_twix(MRSCont.files_ref{kk});
Error in OspreyLoad (line 60)
[MRSCont] = osp_LoadTwix(MRSCont);
Error in osp_onLoad (line 33)
MRSCont = OspreyLoad(MRSCont);
Error while evaluating UIControl Callback.
The code seems to be treating the data as HERMES not MEGA-PRESS judging by the placement of the error (line 401). If I comment out this code, I get an error not much further downstream. If I attempt to run the jobfile using no input for the files_ref, I can load the data, but get an error later in processing. Happy to share these details but they may just be due to the data I’m trying to load in.
Many thanks for your help!
Carolyn McNabb (MRS novice)