fit_svs_edited: Edited SVS 1H brain analysis pipeline.

In spant: MR Spectroscopy Analysis Tools

Edited SVS 1H brain analysis pipeline.

Description

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

Usage

fit_svs_edited(
  input,
  w_ref = NULL,
  output_dir = NULL,
  mri = NULL,
  mri_seg = NULL,
  external_basis = NULL,
  p_vols = NULL,
  format = NULL,
  editing_scheme = NULL,
  invert_edit_on = NULL,
  invert_edit_off = NULL,
  pul_seq = NULL,
  TE = NULL,
  TR = NULL,
  TE1 = NULL,
  TE2 = NULL,
  TE3 = NULL,
  TM = NULL,
  append_basis_ed_off = NULL,
  remove_basis_ed_off = NULL,
  pre_align = TRUE,
  dfp_corr = TRUE,
  output_ratio = NULL,
  ecc = FALSE,
  hsvd_width = NULL,
  decimate = FALSE,
  trunc_fid_pts = NULL,
  fit_opts_edited = NULL,
  fit_opts_ed_off = NULL,
  fit_subset = NULL,
  legacy_ws = FALSE,
  w_att = 0.7,
  w_conc = 35880,
  use_basis_cache = "auto",
  summary_measures = NULL,
  dyn_av_block_size = NULL,
  dyn_av_scheme = NULL,
  dyn_av_scheme_file = NULL,
  plot_ppm_xlim = NULL,
  extra_output = FALSE,
  verbose = FALSE
)

Arguments

input	path or mrs_data object containing MRS data.
w_ref	path or mrs_data object containing MRS water reference data.
output_dir	directory path to output fitting results.
mri	filepath or nifti object containing anatomical MRI data.
mri_seg	filepath or nifti object containing segmented MRI data.
external_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).
format	Override automatic data format detection. See format argument in read_mrs() for permitted values.
editing_scheme	describes the dynamic data ordering. Can be one of: 'on-off-blocks', 'on-off-interleaved', 'off-on-blocks' or 'off-on-interleaved'.
invert_edit_on	set to TRUE to invert the edit-on sub-spectra.
invert_edit_off	set to TRUE to invert the edit-off sub-spectra.
pul_seq	Pulse sequence to use for basis simulation. Can be one of the following values : "press", "press_ideal", "press_shaped", "steam" or "slaser". If "press" then "press_ideal" will be assumed unless the magnetic field is stronger that 2.8 Tesla, "press_shaped" will be assumed for 2.9 Tesla and above.
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.
TE1	PRESS or sLASER sequence timing parameter in seconds.
TE2	PRESS or sLASER sequence timing parameter in seconds.
TE3	sLASER sequence timing parameter in seconds.
TM	STEAM mixing time parameter in seconds.
append_basis_ed_off	names of extra signals to add to the default basis. Eg append_basis_ed_off = c("peth", "cit"). Cannot be used with precompiled basis sets.
remove_basis_ed_off	grep expression to match names of signals to remove from the basis. For example: use "*" to remove all signals, "^mm|^lip" to remove all macromolecular and lipid signals, "^lac" to remove lactate. This operation is performed before signals are added with append_basis_ed_off. Cannot be used with precompiled basis sets.
pre_align	perform simple frequency alignment to known reference peaks.
dfp_corr	perform dynamic frequency and phase correction using the RATS method.
output_ratio	optional string to specify a metabolite ratio to output. Defaults to "tCr". Multiple metabolites may be specified for multiple outputs. Set to NA to omit.
ecc	option to perform water reference based eddy current correction, defaults to FALSE.
hsvd_width	set the width of the HSVD filter in Hz. Note the applied width is between -width and +width Hz, with 0 Hz being defined at the centre of the spectral width. Default is disabled (set to NULL), 30 Hz is a reasonable value.
decimate	option on decimate the data by a factor of 2 before analysis. Defaults to FALSE.
trunc_fid_pts	number of points to truncate the input data by in the time-domain. E.g. setting to 1024 will ensure data with more time-domain points will be truncated to a length of 1024. Defaults to NULL, where truncation is not performed.
fit_opts_edited	options to pass to the fitting method for the edited spectrum.
fit_opts_ed_off	options to pass to the fitting method for the edit-off spectrum.
fit_subset	specify a subset of dynamics to analyse, for example 1:16 would only fit the first 16 dynamic scans.
legacy_ws	perform and output legacy water scaling compatible with default LCModel and TARQUIN behaviour. See w_att and w_conc arguments to change the default assumptions. Default value is FALSE.
w_att	water attenuation factor (default = 0.7) for legacy water scaling. Assumes water T2 of 80ms and a TE = 30 ms. exp(-30ms / 80ms) ~ 0.7.
w_conc	assumed water concentration (default = 35880) for legacy water scaling. Default value corresponds to typical white matter. Set to 43300 for gray matter, and 55556 for phantom measurements.
use_basis_cache	Pre-cache basis sets to reduce analysis speed. Can be one of the following : "auto", "all" or "none". The default value of "auto" will only use the cache for 3T PRESS - which generally requires more detailed simulation due to high CSD.
summary_measures	output an additional table with a subset of metabolite levels, eg c("tNAA", "tNAA/tCr", "tNAA/tCho", "Lac/tNAA").
dyn_av_block_size	perform temporal averaging with the specified block size. Defaults to NULL, eg average across all dynamic scans.
dyn_av_scheme	a numeric vector of sequential integers (starting at 1), with the same length as the number of dynamic scans in the metabolite data. For example: c(1, 1, 2, 1, 1, 3, 1, 1).
dyn_av_scheme_file	a file path containing a single column of sequential integers (starting at 1) with the same length as the number of dynamic scans in the metabolite data. File may be formatted as .xlsx, .xls, text or csv format.
plot_ppm_xlim	plotting ppm axis limits in the html results. results.
extra_output	write extra output files for generating custom plots. Defaults to FALSE.
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")
out_dir <- file.path("~", "fit_svs_result")
## Not run: 
fit_result <- fit_svs(metab, w_ref, out_dir)

## End(Not run)

spant documentation built on April 4, 2025, 1:40 a.m.