spm12_slice_timing: SPM12 Slice Timing Correction

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

Description

Performs SPM12 slice timing correction on images

Usage

spm12_slice_timing(filename, time_points = NULL, nslices, tr, ta = tr -
  tr/nslices, slice_order = 1:nslices, ref_slice, prefix = "a",
  add_spm_dir = TRUE, spmdir = spm_dir(verbose = verbose, install_dir =
  install_dir), clean = TRUE, verbose = TRUE, outdir = tempdir(),
  retimg = FALSE, reorient = FALSE, install_dir = NULL, ...)

build_spm12_slice_timing(filename, time_points = NULL, nslices, tr,
  ta = tr - tr/nslices, slice_order = 1:nslices, ref_slice,
  prefix = "a", add_spm_dir = TRUE, spmdir = spm_dir(verbose =
  verbose, install_dir = install_dir), clean = TRUE, verbose = TRUE,
  outdir = tempdir(), install_dir = NULL, ...)

Arguments

filename	Files to be slice-time corrected
time_points	A vector of time points to run slice-time correction. If filename is a 4D file, then will do all the time points. Otherwise, filename must be a character vector of 3D files or a list of 3D nifti objects.
nslices	Number of slices in the images
tr	Repetition time (in seconds)
ta	Time between the first and the last slice within one scan
slice_order	Order slices were taken (if not specified, assumed ascending), bottom slice = 1
ref_slice	Reference slice
prefix	Prefix to append to front of image filename
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
verbose	Print diagnostic messages
outdir	Directory to copy results
retimg	(logical) return image of class nifti
reorient	(logical) If retimg, should file be reoriented when read in? Passed to readNIfTI.
install_dir	directory to download SPM12
...	Arguments passed to run_spm12_script

Value

List of results, the SPM job, the script and the outfile

neuroconductor/spm12r documentation built on May 19, 2021, 6:31 a.m.