Apply Warp from FNIRT

This function applies a coefficient map from fnirt to other images

fsl_applywarp(
  infile,
  reffile,
  warpfile,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

infile

(character) input filename

reffile

(character) reference image to be registered to

warpfile

(character) reference image to be registered to

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

opts

(character) additional options to FLIRT

verbose

(logical) print out command before running

...

additional arguments passed to readnii.

Value

character or logical depending on intern