spm12_normalize_write: SPM12 Normalize (Write)

Description Usage Arguments Value Examples

View source: R/spm12_normalize_write.R

Description

Applies SPM12 (Spatial) Normalization to images

Usage

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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

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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 Sept. 3, 2018, 9:04 a.m.