Create basis of Siemens 1.5T for FSL-MRS

MRS Software
1

Dear all,

I would like to create MRS basis set in FSL-MRS JSON format using data acquiring from Siemens 1.5T svs_se PRESS. Here is the scan parameters.
B0=1.5, TR=1500, TE=30, Sample size = 1024

Here is what I tried so far.
Use MRICloud: it might not support 1.5T.

Use GitHub - shui5/MRSCloud: MRS Simulation and change “FieldStr”: [“1.5T”]:

Error in [load_parameters_1_5T](matlab:matlab.lang.internal.introspective.errorDocCallback(‘load_parameters_1_5T’, ‘/MATLAB Drive/MRSCloud-main/functions/load_parameters_1_5T.m’, 320)) ([line 320](matlab: opentoline(‘/MATLAB Drive/MRSCloud-main/functions/load_parameters_1_5T.m’,320,0))) refRF = io_loadRFwaveform(refocWaveform,‘ref’,0); ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Error in [run_simulations_cloud](matlab:matlab.lang.internal.introspective.errorDocCallback(‘run_simulations_cloud’, ‘/MATLAB Drive/MRSCloud-main/run/run_simulations_cloud.m’, 111)) ([line 111](matlab: opentoline(‘/MATLAB Drive/MRSCloud-main/run/run_simulations_cloud.m’,111,0))) MRS_temp = load_parameters_1_5T(MRS_temp); % This is the function you need to edit to change the simulation parameters (not specified above this line)

Use https://juchem.bme.columbia.edu/content/mr-spectroscopy-basis-sets.

  1. Download RawBasis_for_PRESSSiemens_TE_30_BW_2500_NPts_1024
  2. Run basis_tools convert RawBasis_for_PRESSSiemens_TE_30_BW_2500_NPts_1024 --fieldstrength 1.5 RawBasis_for_PRESSSiemens_TE_30_BW_2500_NPts_1024_basis
  3. Run fsl_mrs --data fsl_mrs_proc/metab.nii.gz
    –basis RawBasis_for_PRESSSiemens_TE_30_BW_2500_NPts_1024_basis
    –output fsl_mrs_fit
    –report
Traceback (most recent call last):
  File "/Users/hungyu/fsl/bin/fsl_mrs", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/Users/hungyu/fsl/lib/python3.12/site-packages/fsl_mrs/scripts/fsl_mrs.py", line 295, in main
    conjugated = mrs.check_Basis(repair=True)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/hungyu/fsl/lib/python3.12/site-packages/fsl_mrs/core/mrs.py", line 626, in check_Basis
    basis = self.basis
            ^^^^^^^^^^
  File "/Users/hungyu/fsl/lib/python3.12/site-packages/fsl_mrs/core/mrs.py", line 231, in basis
    return self._basis.get_formatted_basis(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/hungyu/fsl/lib/python3.12/site-packages/fsl_mrs/core/basis.py", line 238, in get_formatted_basis
    formatted_basis = self._resampled_basis(1 / bandwidth, points)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/hungyu/fsl/lib/python3.12/site-packages/fsl_mrs/core/basis.py", line 327, in _resampled_basis
    raise BasisHasInsufficentCoverage('The basis spectra covers too little time. '
fsl_mrs.core.basis.BasisHasInsufficentCoverage: The basis spectra covers too little time. Please reduce the dwelltime, number of points or pad this basis.

Due to limited resource for 1.5T from internet, please let me know any possible solution to get basis for FSL-MRS on 1.5T MRI.

Thanks.