spm12_normalize: SPM12 Normalize (Estimate and Write)

In muschellij2/spm12r: Wrapper Functions for 'SPM' (Statistical Parametric Mapping) Version 12 from the 'Wellcome' Trust Centre for 'Neuroimaging'

SPM12 Normalize (Estimate and Write)

Description

Performs SPM12 (Spatial) Normalization on an Image

Usage

spm12_normalize(
  filename,
  other.files = NULL,
  bounding_box = matrix(c(-90, -126, -72, 90, 90, 108), nrow = 2, byrow = TRUE),
  biasreg = 0.001,
  biasfwhm = 60,
  regularization = c(0, 0.001, 0.5, 0.05, 0.2),
  affine = c("mni", "eastern", "subj", "none", ""),
  smoothness = 0,
  sampling_distance = 3,
  voxel_size = c(2, 2, 2),
  interp = c("bspline4", "nearestneighbor", "trilinear", paste0("bspline", 2:3),
    paste0("bspline", 5:7)),
  add_spm_dir = TRUE,
  spmdir = spm_dir(verbose = verbose, install_dir = install_dir),
  clean = TRUE,
  verbose = TRUE,
  install_dir = NULL,
  ...
)

Arguments

filename	File to be normalized to the template
other.files	Files to be written using the estimated normalization
bounding_box	matrix (2x3) of the bounding box to use. Default is for MNI 2mm template size
biasreg	Amount of bias regularization
biasfwhm	FWHM of Gaussian smoothness of bias.
regularization	parameters for warping regularization
affine	Space to register the image to, using an affine registration
smoothness	FWHM of smoothing done
sampling_distance	smoothness of the warping field. This is used to derive a fudge factor to account for correlations between neighbouring voxels. Approximate distance between sampled points when estimating the model parameters.
voxel_size	The voxel sizes (x, y & z, in mm) of the written normalised images.
interp	Interpolator for sampling in fixed space
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
install_dir	directory to download SPM12
...	Arguments passed to run_spm12_script

Value

List of output filenames

muschellij2/spm12r documentation built on Aug. 31, 2022, 9:49 p.m.