Problem loading .rda files

Dear experts,

I am quite new to spectroscopy and have a few questions.

  1. For TWIX data, I was able to run the whole process without any problems. However, my question would be how define which data needs to be discarded, how to find artifacts or outliers? Is there a good description somewhere how to evaluate the data?

  2. Unfortunately I only have twix data for 4 participants. The whole study was recorded 2 years ago (not from me) and they only find out that twix would be better at the end of the experiment. For all other 13 participants, I only had rda files. I had some problems loading the rda files into Osprey. I put ON / OFF and DIFF into one folder for each subject separately and loaded that one in the jobRDA file. I further modified the files(counter) variable that all three files were uploaded. But independet of the fact if one or all three were uploaded, there was an error in Matlab during the loading of the data.

  1. I had several runs for each participant with the same settings. Is there a way to include different runs or to sum them up within the software?

Any help would be really appreciated.

best regards,
Tina

Hi Tina,

Thanks for using Osprey! Happy to assist:

  1. It’s difficult to come up with hard cut-off exclusion criteria, and I tend to advise against that. If you’re looking for quantitative numbers, the SNR and FWHM (signal-to-noise ratio and linewidth) that Osprey returns are valuable indicators of data quality, as are the fit residuals. Generally, you want to see a fit model that agrees well with the data you’re trying to fit - gross modeling artefacts are a sure sign that something went wrong. In terms of artefacts, Roland Kreis’ artefact gallery is still a wonderful resource.
  2. Don’t use the DIFF files at all when loading MEGA-PRESS data; just put the ON and OFF in the same folder. Let me know if that fixes your problems. (Needless to say that you need to keep a keen eye on subtraction artefacts with RDA data!)
  3. We have something like that under development, but not quite ready for release yet (It’s certainly possible using existing FID-A functions!).

Cheers!
Georg

Hi Georg,

thanks for your response and the very helpful link to the artefact gallery. I will have a look on that.

I deleted the DIFF files from the folder, but still got the same error message, that something with the plot does not work (see previous message) .

I tried the same with the original DICOMS instead of the rda files. There the data loading works, however the processing leads to an error:

Any ideas what went wrong here?

Best regards,
Tina

Hi Tina,

Has Helge been in touch with you about this particular problem? Can you share a screenshot of your folder organization and post the file specification sections of the job file you’ve been using?

Thanks,
Georg

Hi Georg,

thanks for getting back to this issue. Yes, Helge was also in touch. I found a solution to concatenate the different runs using the fid-a functions. Thus, this works now for the twix files.

Still, I have the problems during loading the rda files, leading to the error message posted in my first comment.

My folder structure looked like this:

The jobfile like this (sorry, I was not able to upload the .m file, thus I made a .doc out of it). To the original jobRDA file I added a task loop, since my data was a bit different structured to the example. But this loop works well with the twix files, thus, I am not sure if that is the problem.

jobRDA.docx (22.9 KB)

Best regards,
Tina

Hi Georg,

I tried to figure out where the problem is in my data. One problem could be solved (the one with the “fids”) mentioned in my second post.

Still the first one with the plot is still there. Running the matlab code line by line I found out, that my spec data only has dimension 281 x 2 (with complex numbers) instead of three dimensions: extracted out of “osp_plotLoad.m”

Thus, it can not access the specs(:,rr,2). Further, the number of averages calculated out of the data is 32. But the loop is not able to run beyond 2 because of the problem with the dimensions. Is there something wrong with my data?

Further, the variable “stag” seems to be 0 in my case and also only has one dimension. Thus, stag(2) would also not work. Did I do something wrong here?

Best regards,
Tina

I think the easiest way to look at this is for you to share a de-identified dataset with me via e-mail. Could you do that? Thanks :slight_smile:

I will send you an email with the link to the dataset.
Thanks a lot!