RNiftyReg (version 2.0.0)

niftyreg: Two and three dimensional image registration

Description

The niftyreg function performs linear or nonlinear registration for two and three dimensional images. 4D images may also be registered volumewise to a 3D image, or 3D images slicewise to a 2D image. This function is a common wrapper for niftyreg.linear and niftyreg.nonlinear.

Usage

niftyreg(source, target, scope = c("affine", "rigid", "nonlinear"),
  init = NULL, sourceMask = NULL, targetMask = NULL, symmetric = TRUE,
  estimateOnly = FALSE, ...)
## S3 method for class 'niftyreg':
as.array(x, ...)

Arguments

source

The source image, an object of class "nifti" or "internalImage", or a plain array, or a NIfTI-1 filename. Must have 2, 3 or 4 dimensions.

target

The target image, an object of class "nifti" or "internalImage", or a plain array, or a NIfTI-1 filename. Must have 2 or 3 dimensions.

scope

A string describing the scope, or number of degrees of freedom (DOF), of the registration. The currently supported values are "affine" (12 DOF), "rigid" (6 DOF) or "nonlinear" (high DOF, with the exact number dependi

init

Transformation(s) to be used for initialisation, which may be NULL, for no initialisation, or an affine matrix or control point image (nonlinear only). For multiple registration, where the source image has one more dimension than the target,

sourceMask

An optional mask image in source space, whose nonzero region will be taken as the region of interest for the registration. Ignored when symmetric is FALSE.

targetMask

An optional mask image in target space, whose nonzero region will be taken as the region of interest for the registration.

symmetric

Logical value. Should forward and reverse transformations be estimated simultaneously?

estimateOnly

Logical value: if TRUE, transformations will be estimated, but images will not be resampled.

...

Further arguments to niftyreg.linear or niftyreg.nonlinear.

x

A "niftyreg" object.

Value

• A list of class "niftyreg" with components:
• image
  An array representing the registered and resampled source image in the space of the target image. This element is NULL if the estimateOnly parameter is TRUE.
• forwardTransforms
  A list of (linear or nonlinear) transformations from source to target space.
• reverseTransforms
  A list of (linear or nonlinear) transformations from target to source space.
• iterations
  A list of integer vectors, giving the number of iterations completed at each ``level'' of the algorithm. Note that for the first level of the linear algorithm specifically, twice the specified number of iterations is allowed.
• source
  An internal representation of the source image for each registration.
• target
  An internal representation of the target image.
• The as.array method for this class returns the image element.

References

Please see niftyreg.linear or niftyreg.nonlinear for references relating to each type of registration.

See Also

niftyreg.linear and niftyreg.nonlinear, which do most of the work. Also, forward and reverse to extract transformations, and applyTransform to apply them to new images or points.

Examples

source <- readNifti(system.file("extdata", "epi_t2.nii.gz",
  package="RNiftyReg"))
target <- readNifti(system.file("extdata", "flash_t1.nii.gz",
  package="RNiftyReg"))

result <- niftyreg(source, target, scope="affine")