suspect.fitting API Reference

suspect.fitting.attenuation_scaling_factor(t1, t2, te, tr)

Calculates the expected attenuation in an MRS signal arising due to T1 and T2 effects, according to the equation: \(\mathrm{e}^{-\frac{TE}{T2}}(1 - \mathrm{e}^{-\frac{TR}{T1}})\)

Parameters

• t1 – The T1 of the tissue

• t2 – The T2 of the tissue

• te – The echo time of the sequence

• tr – The repetition time of the sequence

Returns

The attenuation factor in the observed signal expected due to T1 and T2 effects

Return type

float

Notes

This function uses the simplified form of the equation, assuming that TE is much shorter than T1 and so the sequence behaves roughly as a 90 pulse followed by a readout, any refocussing pulses do not substantially change the longitudinal magnetisation. If this is not the case then the details of the sequence will be important and a more precise form of this calculation will be required.

suspect.fitting.molar_concentration_factor(f_wm, f_gm, f_csf, te, tr, tissue_params=None)

Calculate the scaling factor necessary to obtain molar metabolite concentrations from a ratio of metabolite to water peak amplitude.

Parameters

• f_wm (float) – The fraction of the voxel containing white matter

• f_gm (float) – The fraction of the voxel containing grey matter

• f_csf (float) – The fraction of the voxel containing CSF

• te (float) – The echo time of the sequence

• tr (float) – The repetition time of the sequence

• tissue_params (dict, optional) – User supplied values for tissue MR properties including T1 and T2

Returns

The scaling factor to convert metabolite to water ratios to molar concentrations.

Return type

float

Notes

The calculation used here follows the form derived in 1.

There are various parameters required for these calculations which can vary, for example with field strength or other conditions. Default values are provided in Suspect (tissue water concentrations are drawn from Gasparovic 2006, relaxation times from Gussew 2012), but they can be overridden by passing in alternative values in the tissue_parameters argument. The relevant parameters are:

Key	Description	Default Value
beta_wm	the water density of white matter	0.65
beta_gm	the water density of grey matter	0.78
beta_csf	the water density of CSF	0.97
h2o_t1_wm	the T1 of water in white matter	1080ms
h2o_t1_gm	the T1 of water in grey matter	1820ms
h2o_t1_csf	the T1 of water in CSF	4160ms
h2o_t2_wm	the T2 of water in white matter	70ms
h2o_t2_gm	the T2 of water in grey matter	100ms
h2o_t2_csf	the T2 of water in CSF	500ms
met_t1	the T1 of metabolites in brain tissue	1400ms
met_t2	the T2 of metabolites in brain tissue	200ms

References

1

Near, J., Harris, A. D., Juchem, C., Kreis, R., Marjańska, M., Öz, G., et al. (2020). Preprocessing, analysis and quantification in single‐voxel magnetic resonance spectroscopy: experts’ consensus recommendations. NMR in Biomedicine, 29, 323–23. http://doi.org/10.1002/nbm.4257

suspect.fitting.tarquin.process(data, wref=None, aq_factor=None, options={})

Runs the Tarquin basis set fitting program to determine metabolite concentrations.

Parameters

• data (MRSData) – The water suppressed FID data to be fitted.

• wref (MRSData) – Optional water reference file for concentration scaling.

• aq_factor (float) – Absolute quantification factor.

• options (dict) – Set of Tarquin parameters to override.

Returns

Output from running Tarquin on the data

Return type

dict