Hi there!
I have inversion data that I’m trying to quantify in LCModel. I’m using the CHSIMU parameter to create models for the macromolecules, and have included a basis set with my inverted metabolites. The fit is good, however, the water corrected values I’m getting are very low (e.g. 4E-4). I wondered if there was perhaps I setting I was missing? ATTH2O is set to 1 and WCONC is set to 55510.
Any thoughts would be appreciated.
Thanks!
Tiffany
Hi Tiffany!
Are all the concentration estimates low, or just those for the MM?
Any chance you could share a config file or sample output data (either here or by email)?
Without this I’m guessing a bit, but the first thing I’d want to check is whether the scaling reference metabolite (default Cr @ 3ppm, defined by WSMET, WSPPM, N1HMET) is meaningful and behaving as expected? Do you see any errors/warnings in the output? For inversion data, I wonder if AREABA 3 might be your problem (ref page 156 of the LCModel manual)
Otherwise, I’d be looking at is the input supplied to makebasis, checking that AUTOSC, CONC, CONCSD settings are appropriate.
Hope this helps a bit.
Alex.