Functions and classes for representation and analysis of MRS data. This is the main module to use when performing routine analysis of MRS data.
Bases: object
Class for analysis of GABA MRS.
Methods
Parameters: | in_data : str
w_idx : list (optional)
line_broadening : float (optional)
zerofill : int (optional)
filt_method : dict (optional)
spect_method: dict (optional) :
min_ppm, max_ppm : float
sampling_rate : float
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Estimate gaba concentration based on equation adapted from Sanacora 1999, p1045
Ref: Sanacora, G., Mason, G. F., Rothman, D. L., Behar, K. L., Hyder, F., Petroff, O. A., ... & Krystal, J. H. (1999). Reduced cortical -aminobutyric acid levels in depressed patients determined by proton magnetic resonance spectroscopy. Archives of general psychiatry, 56(11), 1043.
Fit a model to the portion of the summed spectra containing the creatine and choline signals.
Parameters: | reject_outliers : float or bool
fit_lb, fit_ub : float
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Fit either a single Gaussian, or a two-Gaussian to the GABA 3 PPM peak.
Parameters: | reject_outliers : float
fit_lb, fit_ub : float
phase_correct : bool
fit_func : None or callable (default None).
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Fit a Gaussian function to the Glu/Gln (GLX) peak at 3.75ppm, +/- 0.15ppm [Hurd2004]. Compare this model to a model that treats the Glx signal as two gaussian peaks. Glx signal at. Select between them based on cross-validation
Parameters: | reject_outliers : float or bool
fit_lb, fit_ub : float
scalefit : boolean
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References
[Hurd2004] | (1, 2) 2004, Measurement of brain glutamate using TE-averaged |
PRESS at 3T
Parameters: | reject_outliers : float or bool
fit_lb, fit_ub : float
scalefit : boolean
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Fit a Lorentzian function to the NAA peak at ~ 2 ppm. Example of fitting inverted peak: Foerster et al. 2013, An imbalance between excitatory and inhibitory neurotransmitters in amyothrophic lateral sclerosis revealed by use of 3T proton MRS
This is used to restore the original state of the fits.
add voxel segmentation info
Parameters: | segfile : str
MRSfile : str
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Bases: object
Class for representation and analysis of single voxel (SV) -PROBE experiments.
Parameters: | in_file : str
line_broadening : float
zerofill : int
min_ppm, max_ppm : float
fit_lb, fit_ub : float
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