Standard SVS 1H brain analysis pipeline. — svs_1h_brain_analysis • Spectroscopy Analysis Tools (spant)

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.