.mat basis file to .json

Analysis / Modeling Basis Sets
1

Hi,

I have used MRSCloud to generate a basis set for Siemens PRESS (Unedited) with TE35. I would like to use FSL-MRS to analyze my data, so I need to change the dataformat from .mat to .json. Is there a tutorial on this? Or a step-by-step guide somewhere? I found the package for MRSCloud convertions here GitHub - shui5/MRSCloud: MRS Simulation. I am guessing, that I am on the right tracks, but I don’t know what are the right functions to call next and if the basis set needs to be modified for FSL-MRS. For example do you need to add MM or Lip?

Thank you in advance!

-Nella

2

Hi @zellavie ,

I don’t currently have a way of doing this conversion, but it should be simple. Could you host the mrs cloud format somewhere so I can take a look?

3

MRSCloud also generates a classic LCModel .basis file - I think you can read that, right?

4

Hi,

Thank you for your quick response.

@wclarke you can find my data here: Funet FileSender

also to answer @admin: MRSCloud didn’t allow me to download the files in .basis. Or at least I couldn’t find the place to decide the fileformat.

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When pressing the download results only .mat files are downloaded. I looked at settings and the MRSCloud tab and couldn’t find where to change this dataformat preference. Where can I find the .basis file?

Best,
Nella

5

Hi @zellavie,

MRSCloud creates .mat files for each metabolite in FID-A format, an Osprey basis set as .mat file, and a .BASIS file for LCModel (see fifth entry in this folder).

Best,
Helge

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6

Aah!
Found it. Thank you so much!

7

@zellavie In which case, try using the basis_tools convert routine to convert the .basis file.