FSL Orient

This function calls fslorient

fslorient(
  file,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

file

(character) image to be manipulated

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 fslorient

verbose

(logical) print out command before running

...

additional arguments passed to readnii.

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.