Hi Georg, @admin
As you know, the LCModel output only shows a single spectrum. Recently I wanted to use the results I got from LCModel to show multiple spectra in my Figure at the same time.（Similar to the following images）：
Best,
Jiayi
Dear Jiayi,
Yes, this is the same data LCModel uses to create its plots, and the only way I’m aware of to achieve what you want. There are a few MATLAB functions out there which can read this data as a starting point, including:
(pretty sure the former is incorporated into Osprey)
I also have a simple Python function, which I’ve made available here:
These may need some adaption depending on your exact purpose – eg, if you hope to extract individual metabolite fits (NEACH>0 in the LCModel config), my Python implementation would need to be extended; unsure about the other implementations.
The vertical scaling may be somewhat arbitrary, depending on your acquisition and any preprocessing – depending on context, you might wish to consider some sort of normalization.
Alex.
Hi Jiayi,
As @alex says correctly, we have a nice little function that reads concentrations, fits, individual metabolite signals etc. from the .table and .coord files.
It’s currently a little buried inside osprey/osp_fitUnEdited.m at develop · schorschinho/osprey · GitHub, but you should be able to take the readLCMFitParams sub-function out of there and tailor it to your needs. If you need a standalone version, let me know and I can probably make that happen.
Best,
Georg
