Constants

The following constants are hardcoded into FSL-MRS and are used in the quantisation module.

Water to tetramethylsilane (TMS) chemical shift

H2O_PPM_TO_TMS     = 4.65

Gyromagnetic ratio of proton:

H1_gamma           = 42.576     # MHz/tesla

Concentration scaling parameters

Tissue water density [0]:

TISSUE_WATER_DENSITY = {'GM':0.78,'WM':0.65,'CSF':0.97}

Molecular mass of water:

H2O_MOLECULAR_MASS = 18.01528   # g/mol

Molality of pure water:

H2O_MOLALITY = 55.51E3    # mmol/kg

Number of protons in water:

H2O_PROTONS = 2

The integrated water signal is referenced to a single reference basis. There are three defaults defined in FSL-MRS, and each are tried in the order listed here. Each possible reference is equivalent to a predetermined number of protons and has associated integration limits. There are:

WATER_SCALING_METAB = ['Cr', 'PCr', 'NAA']
WATER_SCALING_METAB_PROTONS = [5, 5, 3]
WATER_SCALING_DEFAULT_LIMITS = [(2, 5), (2, 5), (1.8, 2.2)]

Relaxation parameters

Values are derived from a survey of the literature. References listed below. Values for metabolites are derived from an average of NAA, Cr and Cho peaks.

T1 (all values in seconds)

T2 (all values in ms)

Code definitions:

STANDARD_T1 = {
'1.5T': {'H2O_WM': 0.630,  # Ref: 16
         'H2O_GM': 1.185,  # Ref: 16
         'H2O_CSF': 3.90,  # Ref: 17
         'METAB': 1.238},  # Ref: 18
'3T': {'H2O_WM': 0.97,  # Ref: 1-6
       'H2O_GM': 1.50,  # Ref: 1-6
       'H2O_CSF': 4.47,  # Ref: 4
       'METAB': 1.29},  # Ref: 2, 7-9
'7T': {'H2O_WM': 1.21,  # Ref: 1-6
       'H2O_GM': 2.05,  # Ref: 1-6
       'H2O_CSF': 4.43,  # Ref: 4
       'METAB': 1.43}}  # Ref: 2, 7-9

STANDARD_T2 = {
    '1.5T': {'H2O_WM': 0.080,  # Ref: 19
            'H2O_GM': 0.083,  # Ref: 19
            'H2O_CSF': 2.000,  # Approximate
            'METAB': 0.279},  # Ref: 20
    '3T': {'H2O_WM': 0.073,  # Ref: 1,3,10-11
        'H2O_GM': 0.088,  # Ref: 1,3,10-11
        'H2O_CSF': 2.030,  # Ref: 12
        'METAB': 0.194},  # Ref: 7-9,13-15
    '7T': {'H2O_WM': 0.055,  # Ref: 1,3,10-11
        'H2O_GM': 0.050,  # Ref: 1,3,10-11
        'H2O_CSF': 1.050,  # Ref: 12
        'METAB': 0.131}}  # Ref: 7-9,13-15

References

[0]

Kreis R, Ernst T, Ross BD. Absolute quantitation of water and metabolites in the human brain. II. Metabolite concentrations. J Magn Reson B. 1993;102:9-19.

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Isobe et al. doi: 10.1016/S0730-725X(02)00500-3 - Table 1 mean of metabolites.