Dear community,
I have some data that has been pre-processed with FSLMRS, so it is in MRS nifti format. For comparison reasons, I would also like to fit these data using LCModel.
Do you guys have any tips or maybe even scripts to do this easily?
Thank you!
There is a function in FSL to save out RAW files. See fsl_mrs/utils/mrs_io/lcm_io.py · master · FSL / fsl_mrs · GitLab, which you can get to by from fsl_mrs.utils import mrs_io and then mrs_io.lcm_io.saveRAW. You have to pull the right bits from a NIfTI-MRS object for the saveRAW function arguments, but it gets you some of the way there.
You can also directly load NIfTI-MRS data into Osprey and set up the job file so that Osprey calls the LCModel fitting routine. It will automatically write out all the control files for you and re-import the results from the LCModel output files. You can provide a custom basis set and control file template as well. I suppose that would take care of most of the overhead required to batch an LCM analysis.
LMK how we can help.