Question about osprey gui

Hello, everybody!
I am a novice using Osprey, and I have encountered some problems when quantifying my own data. For my own 7Tsteam, I use the basisset that comes with the software, and the quantification method is lcmodel. I would like to ask:

  1. Why can’t I check some metabolites when I use the GUI? Similar to Figure 1, my basis set is not selected, right?
  2. Is there a better way to generate a basis set suitable for Osprey?
  3. I also want to know the quality of my results data now. What needs to be improved?
    If there are any missing documents, I will fill them as soon as possible.
    Thank you.

    1.pdf (508.8 KB)

Hi @Jude,

I’ll just respond to this question for now, since it’s the most important to deal with. Something does not look right with your data (see a copy below, for completeness). Could you please also show the output of the Raw and Processed tabs in Osprey?

Skjermbilde 2023-11-14 kl. 14.20.48

Thank you for replying to me so quickly, as shown below.
Yes, it’s all loaded
2.pdf (1.1 MB)

Thanks. This data is not usable as is, but so far it’s not clear to me what has gone wrong. Perhaps @Helge has some ideas?

Is this a Siemens system? Just to be sure, I assume it’s in-vivo, proton, brain? If you are able to share some deidentified data I could take a closer look, in case there’s an issue with the import.

Hello, thank you for replying to me so quickly, I don’t know exactly what the data you are talking about to identify, I sent out the graph after processing. If there is any data that needs to be provided, I will also provide it. I wonder if it’s because we didn’t choose the basis set to use correctly for our data.
3.pdf (611.9 KB)
4.pdf (63.6 KB)


Your metabolite spectra should look something like this (figure borrowed from Wijtenburg et al 2013).

Skjermbilde 2023-11-15 kl. 15.31.30

What you have is unrecognisable, both before and after processing. The basis set isn’t an issue here; either something went wrong with the acquisition, or the function for reading the data has failed. Your water reference looks basically alright, so I think there’s a problem specific to the metabolite acquisition.

If it’s possible for you to share some of the incoming twix (.dat) files after removing any subject information, that might help to diagnose the problem.