FSL Orient to MNI

This function calls fslreorient2std

fslreorient2std(
  file,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  verbose = TRUE,
  opts = "",
  ...
)

fslreorient2std_mat(
  file,
  matfile = tempfile(fileext = ".mat"),
  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

verbose

(logical) print out command before running

opts

additional options to pass to fslreorient2std

...

additional arguments passed to readnii.

matfile

Output file for the matrix for reorientation

Value

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