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wtclarke / fsl_mrs

Mirror of the FSL-MRS gitlab repository
https://git.fmrib.ox.ac.uk/fsl/fsl_mrs
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HERMES preprocessing #24

Open diramigo opened 10 months ago

diramigo commented 10 months ago

Looking at the fsl_mrs_preproc_edit script, it seems it only works with MEGA-PRESS data at the moment. Are there plans to include HERMES preprocessing in the future?

Alternatively, is it possible to preprocess HERMES in other software, such as Osprey, and fit the data in fsl_mrs?

wtclarke commented 10 months ago

Hi @diramigo For the moment I think we should have a go with the individual tools from fsl_mrs_proc or better even to use the interactive python tools to come up with a script to do this. E.g. section 2.1 here or the process here adapted to editing.

I'm not super familiar with HERMES, but effectively you want to:

  1. Coil combine your data using the water reference.
  2. Split up each editing condition
  3. Align all the transients in each editing condition.
  4. Average the transients in each condition
  5. Perform ECC and any truncation of extra data points from the start of the FID (these can actually happen at any stage)
  6. Perform alignment between the editing conditions.
  7. Perform the Hadamard encoding stage (this might need a custom bit of script).
diramigo commented 10 months ago

Alright. I will look into the fsl_mrs_preproc_edit script and see if I can use the existing tools to preprocess our HERMES data and perform the appropriate subtraction of sub-spectra. I will post an update here if I make any progress