Applies FLIRT then FNIRT transformations

Source: R/fnirt.R

Applies an affine transformation with FLIRT then the warp image with FNIRT

fnirt_with_affine_apply(
  infile,
  reffile,
  flirt.omat = NULL,
  flirt.outfile = NULL,
  fnirt.warpfile = NULL,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  flirt.opts = "",
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

infile

(character) input filename
reffile

(character) reference image to be registered to
flirt.omat

(character) Filename of output affine matrix
flirt.outfile

(character) Filename of output affine-registered image
fnirt.warpfile

(character) Filename of warp image from fnirt
outfile

(character) output filename
retimg

(logical) return image of class nifti
reorient

(logical) If retimg, should file be reoriented when read in? Passed to readnii.
intern

(logical) pass to system
flirt.opts

(character) additional options to FLIRT
opts

(character) additional options to FNIRT
verbose

(logical) print out command before running
...

additional arguments passed to readnii.

Value

character or logical depending on intern

See also

fnirt_with_affine