spm12_normalize.RdPerforms 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, ... )
| 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 |
List of output filenames