Register using FLIRT

Source: R/fslhd.R

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