Basis set simulation for sLaser 110 TE

Analysis / Modeling Basis Sets
1

Dear Developers,

I am a beginner in MRS signal processing. We have a 3T GE scanner that we use for scientific projects besides everyday clinical work. I use Osprey for quantification of the general MRS applications (PROBE-p TE=35 and 144). It works perfectly.
I am very much interested in 2HG quantification, and I set up a sLaser sequence with 110 TE for this project. I tried to simulate the basis sets using two different approaches:

  1. I used the MATLAB code BasisSetSimulation by Jessica Archibald. In this case, I received basis sets shifted by about -2ppm. I assume that the problem would be the center frequency; however, it is set to 2.02, which is the correct value in my case (if I am not mistaken…). Do you have any idea what could be the problem?
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  1. In parallel, I also tried MRSCloud. Unfortunately, I could not figure out how to transform the .RAW format to .mat. Is there any way to do it? In other basis set simulators, I had to be very specific with the measurement parameters, but not with MRSCloud. What is the reason for this? It didn’t even ask for the B0 field strength. Do I complete the “missing” data while applying the .RAW format?

Which one is the better, more reliable method? Do you have any further suggestions how I can progress?

Best,
András

2

Hi András,

I am happy to comment on our MATLAB BasisSetSimulation code.

From what you show here, I would first check whether you are plotting the final processed basis set or one of the intermediate MATLAB outputs. You can also look at the final generated .PDF

We’ve tested a simulation with your settings and the results look good.

There is a function in FID-A that can help you conver the .raw to .mat inputOutput/io_readlcmraw_dotraw.m

I hope this helps!

3

Dear Jessica,

Thank you for the suggestions!
I checked the final pdf and the individual metabolite spectra as well, and all of them seemed to be fine.
I used Osprey to create the basis.mat file for further application (fit_makeBasis.m). This is where the spectrum somehow shifts, I had attached that shifted plot to my original post. I also realised that your code has the centreFreq variable, while the Osprey code searches for centerFreq. When I replaced centerFreq to centreFreq in the Opsrey code, the spectrum is shifted even more to the negative direction (see below). If I understand well, this is because the code uses a preset centerFreq=3 in the absence of centerFreq tag.

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I guess I can simply try to find a certain centerFreq to get the proper sperctrum, but I am not really convinced by the precision of this strategy. Do you have any idea how I should progress?

Best,
András

4

Hi András,

Thanks for the additional details. For fitting in Osprey, I use this function:

libraries/FID-A/inputOutput/io_LCMBasis.m to convert the .basis.

With this approach, the metabolite spectra remain correctly aligned in my experience.

5

Dear Jessica,

Thank you very much for your help! The fitting worked properly with the io_LCMBasis.m function. Finally, all the peaks seem to be in the correct locations.

Best,
András