spm12_normalize: SPM12 Normalize (Estimate and Write)

Description Usage Arguments Value

View source: R/spm12_normalize.R

Description

Performs SPM12 (Spatial) Normalization on an Image

Usage

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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

smoothingess of the warping field. This is used to derive a fudge factor to account for correlations between neighbouring voxels. Smoother data have more

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


spm12r documentation built on Sept. 3, 2018, 9:04 a.m.