spm12_first_level_spec: SPM12 fMRI First Level Specification

In neuroconductor-devel/spm12r: Wrapper Functions for 'SPM' (Statistical Parametric Mapping) Version 12 from the 'Wellcome' Trust Centre for 'Neuroimaging'

SPM12 fMRI First Level Specification

Description

SPM12 fMRI First Level Specification

Usage

build_spm12_first_level_spec(
  scans = NULL,
  outdir = NULL,
  units = c("scans", "secs"),
  slice_timed = TRUE,
  nslices = NULL,
  ref_slice = NULL,
  tr,
  condition_mat = NULL,
  condition_list = NULL,
  regressor_mat = NULL,
  regressor_list = NULL,
  hpf = 128,
  time_deriv = FALSE,
  disp_deriv = FALSE,
  interactions = FALSE,
  global_norm = c("None", "Scaling"),
  mthresh = 0.8,
  mask = NULL,
  correlation = c("AR(1)", "none", "FAST"),
  n_time_points = NULL,
  verbose = TRUE,
  overwrite = TRUE,
  ...
)

spm12_first_level_spec(
  ...,
  outdir = NULL,
  add_spm_dir = TRUE,
  spmdir = spm_dir(verbose = verbose, install_dir = install_dir),
  clean = TRUE,
  verbose = TRUE,
  overwrite = TRUE,
  install_dir = NULL
)

Arguments

scans	images to run
outdir	output directory for results
units	The onsets of events or blocks can be specified in either scans or seconds.
slice_timed	Were the image slice-time corrected
nslices	If the data were slice-time corrected, the number of slices of the image
ref_slice	If the data were slice-time corrected, the reference slice
tr	The repetition time, in seconds
condition_mat	multiple condition mat/txt file
condition_list	List of conditions: see spm12_condition. This should be a list (or a list of lists) which have the items: name, onset, duration, time_mod_order, param_mod, orth. name does not need to be specified if it is a named list of lists.
regressor_mat	multiple regressor mat/txt file
regressor_list	List of regressors: see spm12_regressor. This should be a list (or a list of lists) which have the items: name, value, and n_time_points. name does not need to be specified if it is a named list of lists.
hpf	High pass filter, in seconds.
time_deriv	time derivative. The time derivative allows the peak response to vary by plus or minus a second.
disp_deriv	dispersion derivative, allows the width of the response to vary.
interactions	Model interactions, Generalized convolution of inputs with basis set.
global_norm	Global intensity normalisation
mthresh	Masking threshold, defined as proportion of globals.
mask	Specify an image for explicitly masking the analysis.
correlation	Serial correlations in fMRI time series
n_time_points	Number of time points
verbose	Print diagnostic messages
overwrite	If a SPM.mat file exists in the outdir, should the file be removed?
...	Arguments passed to run_spm12_script
add_spm_dir	Add SPM12 directory from this package
spmdir	SPM dir to add, will use package default directory
clean	Remove scripts from temporary directory after running
install_dir	directory to download SPM12

Value

A list of objects, including an spm object and output files.

neuroconductor-devel/spm12r documentation built on July 3, 2025, 11:53 p.m.