7T sLASER Basis set

Analysis / Modeling Basis Sets
21

@wclarke Hi William,

Here is the section of the code where metabolites are selected. I would like to ask if I want to simulate another chemical substance, such as acetate, and I know its ppm and J-coupling constants, where should I add this information?

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22

hello, Dear Clarke,

I have carefully read the code, but I still have some questions that I hope you can help me.

I would be grateful if you could provide more insights regarding the code (sequences/eja_svs_slaser/generate.py · master · William Clarke / WIN MRS Basis Sets · GitLab):

  1. How should I interpret line 78 in the image below? What does the value 500 represent?
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Thank you very much for your time and help.

Best regards,

Allan

23
  1. In the following code snippet, line 85 has a default parameter of 200. Is it necessary to modify this parameter based on specific situations? Do you have any suggestions for adjusting this parameter?

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  1. In the next code segment, line 88 has a default parameter of 100. Should this parameter be modified according to circumstances? Do you have any recommendations for adjusting it?

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25

Hi @Yushan, You can pass custom spin systems to the fsl_mrs_sim using the -s flag, poining to a json file with the format matched to .e.g. spinSystems.json · master · William Clarke / denMatSim · GitLab

I.e. For a metabolite with two uncoupled spins at 0 and 1 ppm

"my_metabolite":{
        "j": [[0, 0], [0, 0]],
        "shifts": [0.0, 1.0],
        "name": "my_metabolite",
        "scaleFactor": 1}
26

Hi @run4life_lq This line calculates the γB1 (measured in hertz) that the excitation pulse requires to perform a 90 degree excitation. This is referenced to a 1 ms pulse trying to achieve a 180 degree flip, which would require a 500 Hz γB1. So for a 90 degree 1ms pulse the outcome would be 250 Hz, but this is also scaled by the pulse amplitude integral (amp_int_rel).

27

200 points should be reasonable for this sequence.

28

This is just a constant term used for the shaping of the pulses, it shouldn’t be modified. There is some older adiabatic pulse literature on its optimisation.

29

Hi Georg,

I’m currently using MRSCloud website to generate a basis set for my 7T sequence. While exploring the website, I couldn’t find an option to set the field strength.

I also reviewed the source code on GitHub, where it appears possible to specify this setting. However, I encountered an error during the load_parameters step (line 113 of run_simulations_cloud) for both localization sequences. Based on the error messages, it seems to be caused by missing files:

‘Philips_GOIA_WURST_100pts.mat’ for sLASER
‘orig_refoc_mao_100_4.pta’ for PRESS

Are these files available somewhere, or would you be able to share them with me?

Best,
Mingrun

30

@Mingrun, unfortunately, MRSCloud does not support generation of basis sets for 7T. We do not have the actual timings and rf waveform. The .mat and .pta files you specified are the waveforms in MRSCloud for 3T. You may try the following from @wclarke - sequences/eja_svs_slaser · master · William Clarke / WIN MRS Basis Sets · GitLab

Steve

31

@Mingrun

There’s some info on how to use the FSL tools here: FSL-MRS Practical

The scripts that @stevehui linked to will generate you the sequence description and some scripts for you to run to do the simulations. Afraid macromolecules are still an aread that you need to handle yourself.

32

Hi Mingrun,

We don’t share the pulse waveforms because they are intellectual property.

What vendor and exact sequence parameters are you using? I have made a lot of changes to the MRSCloud code that I haven’t been able to merge back yet because we’re not in control of the MRICloud interface and need to wait for someone to be available to work on it. However, if you let me know what you’re running, I can try and see if I can find out the timings for that sequence and simulate it locally.

Cheers,
Georg