spm12_normalize_write: SPM12 Normalize (Write)

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

Description

Applies SPM12 (Spatial) Normalization to images

Usage

spm12_normalize_write(
  deformation,
  other.files = NULL,
  bounding_box = matrix(c(-90, -126, -72, 90, 90, 108), nrow = 2, byrow = TRUE),
  voxel_size = c(2, 2, 2),
  interp = c("bspline4", "nearestneighbor", "trilinear", paste0("bspline", 2:3),
    paste0("bspline", 5:7)),
  retimg = FALSE,
  reorient = FALSE,
  add_spm_dir = TRUE,
  spmdir = spm_dir(verbose = verbose, install_dir = install_dir),
  clean = TRUE,
  verbose = TRUE,
  install_dir = NULL,
  ...
)

build_spm12_normalize_write(
  deformation,
  other.files = NULL,
  bounding_box = matrix(c(-90, -126, -72, 90, 90, 108), nrow = 2, byrow = TRUE),
  voxel_size = c(2, 2, 2),
  interp = c("bspline4", "nearestneighbor", "trilinear", paste0("bspline", 2:3),
    paste0("bspline", 5:7)),
  verbose = TRUE,
  ...
)

Arguments

deformation	Filename of deformation (nifti)
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
voxel_size	The voxel sizes (x, y & z, in mm) of the written normalised images.
interp	Interpolator for sampling in fixed space
retimg	Logical indicating if image should be returned or result from run_matlab_script
reorient	if retimg=TRUE pass to readNIfTI
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 SPM object, results, and output filenames

Examples

dims = rep(10, 3)
temp_nii = array(rnorm(prod(dims)), dim = dims)
temp_nii = oro.nifti::nifti(temp_nii)
res = build_spm12_normalize_write(temp_nii, 
other.files = temp_nii,
install_dir = tempdir())

spm12r documentation built on March 4, 2021, 9:11 a.m.