rpi_orient {fslr}

Reorient an Image to RPI orientation

Description

This function uses fslswapdim to reorient an image

Usage

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))

## Not run: 
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))
}

## End(Not run)


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))