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

3

0.97

1.50

4.47

1.29

7

1.21

2.05

4.43

1.43

References

1-6

1-6

4

2, 7-9

Code definitions:

STANDARD_T1 = { '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 = { '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.

1

Stanisz GJ et al. doi: 10.1002/mrm.20605.

2

Ethofer T et al. doi: 10.1002/mrm.10640.

3

Wansapura JP et al. doi: 10.1002/(SICI)1522-2586(199904)9:4<531::AID-JMRI4>3.0.CO;2-L.

4

Rooney WD et al. doi: 10.1002/mrm.21122.

5

Dieringer MA et al. doi: 10.1371/journal.pone.0091318.

6

Wright PJ et al. doi: 10.1007/s10334-008-0104-8.

7

Mlynárik V et al. doi: 10.1002/nbm.713.

8

Li Y. doi: 10.4172/2155-9937.S1-002.

9

An L et al. doi: 10.1002/mrm.26612.

10

Gelman N et al. doi: 10.1148/radiology.210.3.r99fe41759.

11

Bartha R et al. doi: 10.1002/mrm.10112.

12

Spijkerman JM et al. doi: 10.1007/s10334-017-0659-3.

13

Marjańska M et al. doi: 10.1002/nbm.1754.

14

Träber F et al. doi: 10.1002/jmri.20053.

15

Wyss PO et al. doi: 10.1002/mrm.27067.