Combining 2 or more MEGA PRESS sessions (SIEMENS TWIX)

MRS Software Osprey
1

Hi,

I attempted to combine multiple sessions into a single, averaged MEGA PRESS acquisition for GSH. Based on previous posts, I used the following sequence of commands (see below). The scripts executed without error but did not merge the sessions (it does just processed both sessions).
Do you have any insights on why this might be happening? (The input files are in SIEMENS Twix format.)
Additionally, the example provided in Osprey, jobSDAT_MEGA_Multidataset.m, fails to complete on both my Mac and Linux machines. Error reported is: “Unable to perform assignment because the size of the left side is 2048-by-1 and the size of the right side is 2048-by-2-by-2”

To your knowledge, how could I combine both sessions properly in Osprey ?

Osprey Version: 2.7 (lastest)
Matlab: 2020a/b
OS: Mac 10.14 (and Linux x86_64 GNU/Linux)

MRSCont = OspreyJob(‘XXXX/OspreyJob.json’);
MRSCont = OspreyLoad(MRSCont);
MRSCont = OspreyProcess(MRSCont);
MRSCont = osp_AverageAllDatasetsAlongExtra(MRSCont);
MRSCont = OspreyFit(MRSCont);
MRSCont = OspreyQuantify(MRSCont);
MRSCont = OspreyOverview(MRSCont);

where OspreyJob.json content is:
{
“seqType”: “MEGA”,
“editTarget”: [“GSH”],
“dataScenario”: “invivo”,
“MM3coModel”: “3to2MM”,
“FWHMMM3co”: “”,
“SpecReg”: “RobSpecReg”,
“SubSpecAlignment”: “L2Norm”,
“UnstableWater”: “0”,
“saveLCM”: “1”,
“savejMRUI”: “1”,
“saveVendor”: “1”,
“saveNII”: “0”,
“savePDF”: “1”,
“method”: “Osprey”,
“ECCmetab”: “1”,
“ECCmm”: “1”,
“includeMetabs”: [“full”],
“style”: “Separate”,
“lolim_range”: “0.5”,
“uplim_range”: “4.0”,
“lolim_rangew”: “2.0”,
“uplim_rangew”: “7.4”,
“bLineKnotSpace”: “0.4”,
“fitMM”: “1”,
“basisSet”: “XXXX/BASIS_Siemens_MEGA_PRESS_GSH131_wMM/BASIS_Siemens_MEGA_PRESS_GSH131_wMM.mat”,
“files”: [“XXXX/meas_MID00028_FID23946_eja_svs_mpress_RM_mpfc1.dat”,“XXXX/meas_MID00032_FID23950_eja_svs_mpress_RM_mpfc2.dat”],
“file_stat”: [“”],
“outputFolder”: [“XXXX/analysis/test”]
}

2

Hi @JB_75007,

Excuse the late response - I only just saw this thread. Where does the error that you report occur? Can you print the content of MRSCont.files after OspreyJob?

Thanks,
Georg

3

Hi Georg,

no worries,

Here is the MRSCont.files content after the commands has been ran.

MRSCont.files

ans =

1×2 cell array

{'/Users/rdoc/Desktop/Osprey_Analysis/NOVA_022_twix/meas_MID00074_FID18924_eja_svs_mpress_RM_mpfc1.dat'}    {'/Users/rdoc/Desktop/Osprey_Analysis/NOVA_022_twix/meas_MID00079_FID18929_eja_svs_mpress_RM_mpfc2.dat’}

Thanks !

JB

Commands used:

addpath(genpath(‘/Users/rdoc/fMRI/osprey-v.2.7.0’));
MRSCont = OspreyJob(‘/Users/rdoc/Desktop/Osprey_Analysis/FINAL_ANALYSIS/OspreyJob2.json’);
MRSCont = OspreyLoad(MRSCont);
MRSCont = OspreyProcess(MRSCont);
MRSCont = osp_AverageAllDatasetsAlongExtra(MRSCont);
MRSCont = OspreyFit(MRSCont);
MRSCont = OspreyQuantify(MRSCont);
MRSCont = OspreyOverview(MRSCont);

OspreyJob2.json

{
“seqType”: “MEGA”,
“editTarget”: [“GSH”],
“dataScenario”: “invivo”,
“MM3coModel”: “3to2MM”,
“FWHMMM3co”: “”,
“SpecReg”: “RobSpecReg”,
“SubSpecAlignment”: “L2Norm”,
“UnstableWater”: “0”,
“saveLCM”: “0”,
“savejMRUI”: “0”,
“saveVendor”: “0”,
“saveNII”: “0”,
“savePDF”: “1”,
“method”: “Osprey”,
“ECCmetab”: “1”,
“ECCmm”: “1”,
“includeMetabs”: [“full”],
“style”: “Separate”,
“lolim_range”: “0.5”,
“uplim_range”: “4.0”,
“lolim_rangew”: “2.0”,
“uplim_rangew”: “7.4”,
“bLineKnotSpace”: “0.4”,
“fitMM”: “1”,
“basisSet”: “/Users/rdoc/Desktop/Osprey_Analysis/BASIS_Siemens_MEGA_PRESS_GSH131_wMM/BASIS_Siemens_MEGA_PRESS_GSH131_wMM.mat”,
“files”: [“/Users/rdoc/Desktop/Osprey_Analysis/NOVA_022_twix/meas_MID00074_FID18924_eja_svs_mpress_RM_mpfc1.dat”,“/Users/rdoc/Desktop/Osprey_Analysis/NOVA_022_twix/meas_MID00079_FID18929_eja_svs_mpress_RM_mpfc2.dat”],
“file_stat”: [“”],
“outputFolder”: [“/Users/rdoc/Desktop/Osprey_Analysis/FINAL_ANALYSIS/TMP”]
}