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Commit 87848dcd authored by William Clarke's avatar William Clarke
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Add information on constant values in code.

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docs/user_docs/constants.rst 0 → 100644
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.. _constants:
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}
Mollecular 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
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)
__________________________
.. csv-table::
:header: "Field strength (T)", "Water: WM", "Water: GM", "Water: CSF" , "Metabolites"
:widths: 10, 10, 10, 10, 10
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.
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docs/user_docs/index.rst
View file @ 87848dcd
......@@ -24,5 +24,6 @@ If this is your first experience with FSL-MRS, get started with the :ref:`Quick
quantitation
simulation
visualisation
constants
troubleshooting
changelog
fsl_mrs/utils/constants.py
View file @ 87848dcd
......@@ -14,19 +14,49 @@ H2O_PPM_TO_TMS = 4.65 # Shift of water to Tetramethylsilane
H1_gamma = 42.576 # MHz/tesla
# Concentration scaling parameters
TISSUE_WATER_DENSITY = {'GM':0.78,'WM':0.65,'CSF':0.97} # 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.
TISSUE_WATER_DENSITY = {'GM':0.78,'WM':0.65,'CSF':0.97}
#TISSUE_WATER_DENSITY reference: Ernst T, Kreis R, Ross BD. Absolute Quantitation of Water and Metabolites in the Human Brain. I. Compartments and Water. Journal of Magnetic Resonance, Series B 1993;102:1–8 doi: 10.1006/jmrb.1993.1055.
H2O_MOLECULAR_MASS = 18.01528 # g/mol
H2O_MOLALITY = 55.51E3 # mmol/kg
H2O_PROTONS = 2
# T1 parameters
# Derived from a survey of the literature. References listed below.
# Metabolite values derived from an average of NAA, Cr and Cho peaks.
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
# T2 parameters
# 3T from https://onlinelibrary.wiley.com/doi/epdf/10.1002/nbm.3914
# 7T from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4549223/ - except copied CSF
STANDARD_T2 = { '7T':{'H2O_GM':0.05,
'H2O_WM':0.055,
'H2O_CSF':2.55,
'METAB':0.160},
'3T':{'H2O_GM':0.11,
'H2O_WM':0.08,
'H2O_CSF':2.55,
'METAB':0.271}}
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
'''
T1 & T2 References:
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.
'''
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