rats: Robust Alignment to a Target Spectrum (RATS).

In spant: MR Spectroscopy Analysis Tools

Robust Alignment to a Target Spectrum (RATS).

Description

Robust Alignment to a Target Spectrum (RATS).

Usage

rats(
  mrs_data,
  ref = NULL,
  xlim = c(4, 0.5),
  max_shift = 20,
  p_deg = 2,
  sp_N = 2,
  sp_deg = 3,
  max_t = 0.2,
  basis_type = "poly",
  rescale_output = TRUE,
  phase_corr = TRUE,
  ret_corr_only = TRUE,
  zero_freq_shift_t0 = FALSE,
  remove_freq_outliers = FALSE,
  freq_outlier_thresh = 3,
  remove_phase_outliers = FALSE,
  phase_outlier_thresh = 3,
  remove_amp_outliers = FALSE,
  amp_outlier_thresh = 3
)

Arguments

mrs_data	MRS data to be corrected.
ref	optional MRS data to use as a reference, the mean of all dynamics is used if this argument is not supplied.
xlim	optional frequency range to perform optimisation, set to NULL to use the full range.
max_shift	maximum allowable frequency shift in Hz.
p_deg	polynomial degree used for baseline modelling. Negative values disable baseline modelling.
sp_N	number of spline functions, note the true number will be sp_N + sp_deg.
sp_deg	degree of spline functions.
max_t	truncate the FID when longer than max_t to reduce time taken, set to NULL to use the entire FID.
basis_type	may be one of "poly" or "spline".
rescale_output	rescale the bl_matched_spec and bl output to improve consistency between dynamic scans.
phase_corr	apply phase correction (in addition to frequency). TRUE by default.
ret_corr_only	return the corrected mrs_data object only.
zero_freq_shift_t0	perform a linear fit to the frequency shifts and set the (linearly modeled) shift to be 0 Hz for the first dynamic scan.
remove_freq_outliers	remove dynamics based on their frequency shift.
freq_outlier_thresh	threshold to remove frequency outliers.
remove_phase_outliers	remove dynamics based on their phase shift.
phase_outlier_thresh	threshold to remove phase outliers.
remove_amp_outliers	remove dynamics based on their amplitude change.
amp_outlier_thresh	threshold to remove amplitude outliers.

Value

a list containing the corrected data; phase and shift values in units of degrees and Hz respectively.

spant documentation built on Sept. 11, 2024, 9:13 p.m.