Performs SPM12 (Spatial) Normalization on an Image
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,
...
)File to be normalized to the template
Files to be written using the estimated normalization
matrix (2x3) of the bounding box to use. Default is for MNI 2mm template size
Amount of bias regularization
FWHM of Gaussian smoothness of bias.
parameters for warping regularization
Space to register the image to, using an affine registration
FWHM of smoothing done
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.
The voxel sizes (x, y & z, in mm) of the written normalised images.
Interpolator for sampling in fixed space
Add SPM12 directory from this package
SPM dir to add, will use package default directory
Remove scripts from temporary directory after running
Print diagnostic messages
directory to download SPM12
Arguments passed to run_spm12_script
List of output filenames