Liver lipid quantification using LCModel

Hi Georg @admin ,
First of all, I would like to thank the MRS community for helping me to solve my previous problem, and now I have encountered new difficulties in using LCModel.I used STEAM sequences to acquire liver MR spectral data without water suppression.Here is the Spectrum i have acquired:

Now I want to use LCModel to quantify the amount of liver fat. Do I need to generate a new simulation and make a new basis set using LCModel to quantify the liver lipid content?


Hi Jiayi,

No, you can use the sptype settings for lipid spectra, e.g. sptype=lipid-8 or sptype=liver-11. For lipid spectra, LCModel doesn’t use basis sets, but rather simulates the relevant resonances internally as Gaussians (very much like macromolecules and lipids for brain spectra). The sptype settings specify most of them by default.

See Section 9.3 of the LCModel manual.


Hi Georg @admin ,

When I used ‘sptype=lipid-8’ I got the results for the liver fat quantification, but there was an error reported as follows:

(which PPMST=8.0ppm,PPMEND=-0.7ppm)
When I modify PPMST≥8.0ppm,PPMEND≤-1.0ppm, the following error is reported again:

Can I reduce my PPMEND so that it is slightly greater than -1.0ppm in order to get the results?


You have a dwell time of 2.28e-4 s, i.e. your spectral width is 4386 Hz.
With 400.3172 Hz/ppm, that translates to ~10.96 ppm spectral width.
Assuming water at 4.68 ppm is at the center, your ppm axis runs from 4.68 + 5.48 = 10.16 ppm to 4.68 − 5.48 = −0.8 ppm. The error appears because you can’t enter a ppmend value outside of your spectral width.

(That said, the fit in your first figure looked fine enough to me)

Hi Georg,

Thank you so much for your kind reply!


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