FSL Motion Correction — mcflirt • fslr

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.

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