Problem fitting PRESS-data to model

MRS Software Osprey
1

Hello,
I’m new to processing MRS data and have run into a problem that I was hoping to get some help with.
I have raw MRS from a GE scanner for PRESS analysis that I want to extract glutamate from. I successfully create the jobfile (imbedded below) and then process the data. But when I want to run the modelling I get the error message " There is no appropriate basis set to model your data".

I was under the impression that with GE .7-files there was no need to specify any other MRS files, but do I also need a basis-file?

I am very grateful for any help!

Best,
Jonatan

Jobfile:

{
	"seqType": "unedited",
	"dataScenario": "invivo",
	"MM3coModel": "3to2MM",
	"FWHMMM3co": "",
	"SpecReg": "RobSpecReg",
	"SubSpecAlignment": "L2Norm",
	"UnstableWater": "0",
	"saveLCM": "0",
	"savejMRUI": "0",
	"saveVendor": "0",
	"saveNII": "0",
	"savePDF": "0",
	"method": "Osprey",
	"ECCmetab": "1",
	"ECCmm": "1",
	"includeMetabs": ["default"],
	"style": "Separate",
	"lolim_range": "0.5",
	"uplim_range": "4.0",
	"lolim_rangew": "2.0",
	"uplim_rangew": "7.4",
	"bLineKnotSpace": "0.4",
	"fitMM": "1",
	"files": [ MRS_data/baseline_DLPFC/S001/5/P09728.7",
	 MRS_data/baseline_DLPFC/S002/5/P30208.7",
	 MRS_data/baseline_DLPFC/S003/5/P84992.7",
	 MRS_data/baseline_DLPFC/S004/5/P31232.7",
	 MRS_data/baseline_DLPFC/S005/5/P48640.7"],
	"files_nii": ["/ /T1/S001_T1_Bsl.nii",
	"/ /T1/S002_T1_Bsl.nii",
	"/ /T1/S003_T1_Bsl.nii",
	"/ /T1/S004_T1_Bsl.nii",
	"/ /T1/S005_T1_Bsl.nii"],
	"file_stat": [""],
	"outputFolder": ["/ /MRS_data/Processed/Test"]
}

P09728_Voxel_1_Exp_1_OspreyLoad_mets.pdf (254.3 KB)

P09728_Voxel_1_OspreyProcess_metab_A.pdf (458.7 KB)

2

This looks like GABA-edited MEGA-PRESS data to me (half of the transients have the NAA peak saturated), so you need to specify the sequence information accordingly (seqType = MEGA, editTarget = GABA). We recommend using a stiffer baseline spline (bLineKnotSpace = 0.55) and anchoring the co-edited 3-ppm MM component to the 0.9-ppm signal (MM3coModel= 3to2MM or 3to2MMsoft; FWHMMM3co = 14 Hz).

Note that you will get two estimates for all metabolites, one from the difference spectrum, one from the OFF spectrum, and literature is not clear at all which one of the two is more reliable at separating Glu and Gln. You can always relatively safely report Glx.

3

Specificly regarding the basis set: Osprey has pre-defined basis sets for the most common configurations – the “no appropriate basis set” message can indicate that either your sequence type or the echo time are somehow unusual. In this case, the echo time (TE=68ms) is entirely standard for GABA+ editing, but the sequence type/edit target have been incorrectly specified – as mentioned above.

The “GABA editing” basis sets contain components for the edit-OFF subspectra as well as the edited difference spectrum.