You should almost always call
xform rather calling
xformpoints(reg, points, ...) # S3 method for character xformpoints(reg, points, ...) # S3 method for cmtkreg xformpoints( reg, points, transformtype = c("warp", "affine"), direction = NULL, FallBackToAffine = FALSE, ... ) # S3 method for reglist xformpoints(reg, points, ...) # S3 method for default xformpoints(reg, points, ...)
A registration defined by a matrix, a function, a
cmtkreg object, a
reglist object containing a
sequence of arbitrary registrations, or a character vector specifying
path(s) to registrations on disk (see details).
Nx3 matrix of points
Additional arguments passed to methods
Which transformation to use when the CMTK file contains both warp (default) and affine
Whether to transform points from sample space to reference
space (called inverse by CMTK) or from reference to sample space
(called forward by CMTK). Default (when
NULL is inverse).
Whether to use the affine transformation for points that fail to transform under a warping transformation.
If a list of transformations is passed in, these transformations are
performed in sequence order, such that
xformpoints(c(a,b,c), x) ==
xformpoints(c, (xformpoints(b, xformpoints(a, x))))
Note that the direction of CMTK registrations can be the source of much confusion. This is because CMTK defines the forward direction as the transform required to reformat an image in sample (floating) space to an image in template space. Since this operation involves filling a regular grid in template space by looking up the corresponding positions in sample space, the transformation that is required is (somewhat counterintuitively) the one that maps template to sample. However in neuroanatomical work, one often has points in sample space that one would like to transform into template space. Here one needs the inverse transformation.