Questions and Warnings with .rda files


First of all, thank you for providing this software! It is very well done and easy to use. I looked through the other posts and didn’t see anything matching my concerns, but if for some reason I overlooked a conversation please feel free to point me in that direction.

I began working through the pipeline using 1 participant (water suppressed and non-water suppressed .rda files and T1.nii file) and ran into some things/warnings that made me want to get an expert opinion on. I am able to run through the full pipeline, but I wanted to make sure that nothing described below would be messing up the final analysis. I am using Monterey 12.1 and Matlab R2020b.

  1. When I load the data, the preprocessed raw spectrum is inverted. This is corrected after going through the processing step.

  2. After processing, there is no data for the chemical shift drift.

  3. I am getting warnings after both the model and quantify steps. I had to upload them as txt files because it wasn’t letting me post as it thought I was tagging users since the @ is used in both warnings.

Model Warning

Model Data_Warning.txt (3.7 KB)

Quantify Warning
Quantify_Warning .txt (4.9 KB)

Thanks is advance!

Hi @AnnaKirk,

Thank you for reaching out! Encouraging to hear that you like Osprey and found a way to integrate it into your research.

About your questions:

  1. Having the raw spectra inverted in the load window is not an issue, as long as this is fixed during the processing (as you have already mentioned)
  2. The chemical shift drift is usually generating a trace of the creatine across all transients/averages. However, the RDA file you are processing is already averaged on the scanner, and therefore it is impossible to generate the trace (You can look at the jobSDAT.m example data to get an idea of what this should look like).
  3. The warnings are usually save to be ignored (all of the ones you are reporting are). They refer to some handles that are used during the GUI updates. You should only be concerned about errors.

I hope that answers your questions. Feel free to reach out if experience any issues.


Thank you so much for the quick and direct response!