This function calls fnirt
to register infile to reffile
and either saves the image or returns an object of class nifti, but does
the affine registration first
fnirt_with_affine(infile, reffile, flirt.omat = NULL,
flirt.outfile = NULL, outfile = NULL, retimg = TRUE,
reorient = FALSE, intern = FALSE, flirt.opts = "", opts = "",
verbose = TRUE, ...)
(character) input filename
(character) reference image to be registered to
(character) Filename of output affine matrix
(character) Filename of output affine-registered image
(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
(character) additional options to FNIRT
(logical) print out command before running
additional arguments passed to readnii
.
character or logical depending on intern