Preprocessing : data in Siemens TWIX formax

Hi, I am new to MRS and I’ve met something confusing when preprocessing the data in Siemens TWIX format.
I executed the run_pressproc_auto.m script within the FID-A, and got the result with each metabolic peak at their accurate chemical shifts.

but when I imported the S01_lcm data into LCModel for futher analysis, I noticed that the data had been confusing, with the H2O’ peak appearing to be the exact 4.7 ppm, but the NAA-CH3 peak at 3 ppm. The spectrum seemed to be scaled incorrectly.

Has anyone else met the same thing as me? Thank you in advance.


Hi @Murph,

Welcome to your exciting MRS journey :wink:

The problem that you are describing could be related to wrong numbers in the NUNFI or DELTAT elements of the .RAW file. These should correspond to the number of points in your spectrum and the dwelltime (time between each acquired point). Could you double-check that those are right? Or it is possible that those are not right in the control file of LCModel. You can also check those numbers in the control file.

Another option to do the pre-processing is Osprey (GitHub - schorschinho/osprey: All-in-one toolbox for processing of magnetic resonance spectroscopy data.). You can pre-process the data and use either Osprey’s linear-combination model or if you have installed a compiled version LCModel on your machine you can also call LCModel from within Osprey. Osprey will then automatically write the control and raw file for you and import the results from LCModel back for further quantification.

Let me know if you get stuck,

I’ve solved it with your kind suggestion!! As you said, the incorrect number in the NUNFI and DELTAT is what causes such a confusing result.

Thank you for your help. I really appreciate it.


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