svs_1h_brain_analysis {spant}

Standard SVS 1H brain analysis pipeline.

Description

Standard SVS 1H brain analysis pipeline.

Usage

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.