svs_1h_brain_analysis_dev: Standard SVS 1H brain analysis pipeline.

In spant: MR Spectroscopy Analysis Tools

Standard SVS 1H brain analysis pipeline.

Description

Note this function is still under development and liable to changes.

Usage

svs_1h_brain_analysis_dev(
  metab,
  w_ref = NULL,
  output_dir = NULL,
  basis = NULL,
  p_vols = NULL,
  append_basis = NULL,
  remove_basis = NULL,
  dfp_corr = FALSE,
  omit_bad_dynamics = FALSE,
  te = NULL,
  tr = NULL,
  output_ratio = "tCr",
  ecc = FALSE,
  abfit_opts = NULL,
  verbose = FALSE
)

Arguments

metab	filepath or mrs_data object containing MRS metabolite data.
w_ref	filepath or mrs_data object containing MRS water reference data.
output_dir	directory path to output fitting results.
basis	precompiled basis set object to use for analysis.
p_vols	a numeric vector of partial volumes expressed as percentages. Defaults to 100% white matter. A voxel containing 100% gray matter tissue would use : p_vols = c(WM = 0, GM = 100, CSF = 0).
append_basis	names of extra signals to add to the default basis. Eg append_basis = c("peth", "cit"). Cannot be used with precompiled basis sets.
remove_basis	names of signals to remove from the basis. Cannot be used with precompiled basis sets.
dfp_corr	perform dynamic frequency and phase correction using the RATS method.
omit_bad_dynamics	detect and remove bad dynamics.
te	metabolite mrs data echo time in seconds. If not supplied this will be guessed from the metab data file.
tr	metabolite mrs data repetition time in seconds. If not supplied this will be guessed from the metab data file.
output_ratio	optional string to specify a metabolite ratio to output. Defaults to "tCr" and multiple metabolites may be specified for multiple outputs. Set as NULL to omit.
ecc	option to perform water reference based eddy current correction, defaults to FALSE.
abfit_opts	options to pass to ABfit.
verbose	output potentially useful information.

Examples

metab <- system.file("extdata", "philips_spar_sdat_WS.SDAT",
                     package = "spant")
w_ref <- system.file("extdata", "philips_spar_sdat_W.SDAT",
                     package = "spant")
## Not run: 
fit_result <- svs_1h_brain_analysis(metab, w_ref, "fit_res_dir")

## End(Not run)

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