Register using FLIRT

This function calls flirt to register infile to reffile and either saves the image or returns an object of class nifti, along with the transformation matrix omat

flirt(
  infile,
  reffile,
  omat = NULL,
  dof = 6,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

infile

(character) input filename

reffile

(character) reference image to be registered to

omat

(character) Output matrix name

dof

(numeric) degrees of freedom (default 6 - rigid body)

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