Dear Georg and Cristina,
Thank you so very much for your replies. I did suspect that the answer might be the differences in how the data is treated in various packages. JMRUI for example has a few manual steps which I am sure had an effect and each participant needs to be pre-processed individually whereas Osprey allows a batch option.
In terms of our project, the data was collected in functional MRS study. One of the aims was to investigate the effect of echo time on the signal. We used PRESS sequence on Philips scanner, TR = 1s; TE = 35ms; TE = 80ms; TE = 140ms; number of acquisitions per block = 720; files in SDAT format. I only analysed TE =35ms with Osprey as other TEs are not currently available in Osprey.
We performed two types of analysis, one as a functional MRS in JMRUI (averaged spectra for each time point of the trial (80 trials)), and another as a static analysis (averaged across the whole block (720 acquisitions in one block)). I repeated static analysis in Osprey and tried to compare the results between these two packages.
All processing steps in JMRUI had to be done separately for each subject and include removal of first 9 acquisitions (leaving 711 acquisitions), alignment, averaging across acquisitions, removal of residual water signal with HLSVD filter (manual step), phase correction with reference file, set reference to NAA, quantitation with QuasarX. Model fit in QuasarX is also a manual step.
Of note, our JMRUI basis set contains smaller number of metabolites than the set in Osprey. I wonder if that could have affected the results.
In terms of Osprey, I went with default options. Perhaps this is were I went wrong!
This is the error I get with one of the corrupted files (or so we thought!)
I hope all of the above makes sense!