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,
...
)
character or logical depending on intern
(character) input filename
(character) reference image to be registered to
(character) Output matrix name
(numeric) degrees of freedom (default 6 - rigid body)
(character) output filename
(logical) return image of class nifti
(logical) If retimg, should file be reoriented when read in?
Passed to readnii
.
(logical) pass to system
(character) additional options to FLIRT
(logical) print out command before running
additional arguments passed to readnii
.