Applies FLIRT then FNIRT transformations

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