Standard SVS 1H brain analysis pipeline.

Standard SVS 1H brain analysis pipeline.

svs_1h_brain_analysis(
  metab,
  basis = NULL,
  w_ref = NULL,
  mri_seg = NULL,
  mri = NULL,
  output_dir = NULL,
  extra = NULL,
  decimate = NULL,
  rats_corr = TRUE,
  ecc = FALSE,
  comb_dyns = TRUE,
  hsvd_filt = FALSE,
  scale_amps = TRUE,
  te = NULL,
  tr = NULL,
  preproc_only = FALSE,
  method = "ABFIT",
  opts = NULL
)

Arguments

metab	filepath or mrs_data object containing MRS metabolite data.
basis	basis set object to use for analysis.
w_ref	filepath or mrs_data object containing MRS water reference data.
mri_seg	filepath or nifti object containing segmented MRI data.
mri	filepath or nifti object containing anatomical MRI data.
output_dir	directory path to output fitting results.
extra	data.frame with one row containing additional information to be attached to the fit results table.
decimate	option to decimate the input data by a factor of two. The default value of NULL does not perform decimation unless the spectral width is greater than 20 PPM.
rats_corr	option to perform rats correction, defaults to TRUE.
ecc	option to perform water reference based eddy current correction, defaults to FALSE.
comb_dyns	option to combine dynamic scans, defaults to TRUE.
hsvd_filt	option to apply hsvd water removal, defaults to FALSE.
scale_amps	option to scale metabolite amplitude estimates, defaults to TRUE.
te	metabolite mrs data echo time in seconds.
tr	metabolite mrs data repetition time in seconds.
preproc_only	only perform the preprocessing steps and omit fitting. The preprocessed metabolite data will be returned in this case.
method	analysis method to use, see fit_mrs help.
opts	options to pass to the analysis method.

Value

a fit_result or mrs_data object depending on the preproc_only option.