FSL Motion Correction

This function calls mcflirt

mcflirt(
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

file	(character) image to be manipulated
outfile	(character) resultant image name (optional)
retimg	(logical) return image of class nifti
reorient	(logical) If retimg, should file be reoriented when read in? Passed to readnii.
intern	(logical) to be passed to system
opts	(character) operations to be passed to mcflirt. Cannot use -o or -verbose, as output file should be specified in outfile.
verbose	(logical) print out command before running
...	additional arguments passed to readnii.

Value

If retimg then object of class nifti. Otherwise, it will have additional attributes in the additional_files field.