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)

Field strength (T)	Water: WM	Water: GM	Water: CSF	Metabolites
1.5	0.63	1.19	3.90	1.24
3	0.97	1.50	4.47	1.29
7	1.21	2.05	4.43	1.43
References	1-6, 16	1-6, 16	4, 17	2, 7-9, 17

T2 (all values in ms)

Field strength (T)	Water: WM	Water: GM	Water: CSF	Metabolites
1.5	80	83	2000	279
3	73	88	2030	194
7	55	50	1050	131
References	1-3, 10-11, 19	1-3, 10-11, 19	12, -	7-9, 13-15, 20

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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Wright PJ et al. doi: 0.1007/s10334-008-0104-8. Table 2 average

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Yamashiro et al. 10.1002/acm2.12659. Table 2 average

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Ratiney et al. doi: 10.1007/s10334-007-0076-0 - Table 3, mean

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[20]

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