rpi_orient: Reorient an Image to RPI orientation

In muschellij2/fslr: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

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))

muschellij2/fslr documentation built on May 10, 2024, 2:12 a.m.