So I recently started working with FSL-MRS for processing SVS data that was acquired in my lab.
Most of the steps were ok but I have encountered some difficulty related to my basis sets and the fitting of the data. I even followed some suggestions on the forum which said trying to conjugate the basis sets and adding MM into the basis sets.
I have attached the final output report. Can someone please help me figure out why my metabolite fit doesn’t seem to be correct?
It looks like from the basis spectra summary that the basis set has the wrong shifts in it. You can see that Lactate is at 2 ppm rather than about 1.3 ppm. Is this basis set for the right field strength? Or otherwise, where did you source it from?
Hi @wclarke
So I had found two other discussions on this where they had similar basis set issues and I got the basis file from https://juchem.bme.columbia.edu/content/mr-spectroscopy-basis-sets
But the BW for my data is 2000 and I used the 2500 press basis for my analysis. I wasn’t really sure what to do because the LCmodel set is encrypted and just followed another discussion I saw on the forum to see if I could fix the fit but nothing seems to work.
What bandwidth did you set when converting the basis to FSL format (using basis_tools convert)? It should be set to the basis set BW (2500) rather than the data (2000).
Hi !
So I had converted the basis set using this same code and I kept the bandwidth as 2500 itself. I did not change it to 2000
So even after following all the steps the same, the fit still wasn’t correct
