Reorient an Image to RPI orientation

Source: R/rpi_orient.R

This function uses fslswapdim to reorient an image

rpi_orient(file, verbose = TRUE)

rpi_orient_file(file, verbose = TRUE)

is_rpi(file, verbose = FALSE)

is.rpi(file, verbose = FALSE)

Arguments

file

Object of class nifti or character path

verbose

print diagnostic messages

Value

List of 3 elements

  • img: Reoriented image of class nifti

  • convention: Convention (Neurological/Radiological) of original image

  • orientation: Original image orientations

Note

`orient_rpi` and `orient_rpi_file` uses `RNifti` to ensure the reading orientation

Examples

lr_fname = system.file( "nifti", "mniLR.nii.gz", package = "oro.nifti")
img = readnii(lr_fname)

rl_fname = system.file( "nifti", "mniRL.nii.gz", package = "oro.nifti")
rl_img = readnii(rl_fname)
stopifnot(all(rl_img[nrow(rl_img):1,,] == img))

if (FALSE) {
if (have_fsl()) {


reor = rpi_orient(rl_fname)
rev = reverse_rpi_orient(reor$img, convention = reor$convention,
orientation = reor$orientation)
stopifnot(all(rev == rl_img))
}
}


reor = orient_rpi(rl_fname)
stopifnot(all(img == reor$img))

rev = reverse_orient_rpi(reor$img, convention = reor$convention,
orientation = reor$orientation)
stopifnot(all(rev == rl_img))