Extract permutation matrix associated with an image

A permutation matrix defines how the native voxel coordinates can be transformed to standard (LPI) orientation.

Usage

perm_mat(x, ...)

# S4 method for class 'AxisSet2D'
perm_mat(x, ...)

# S4 method for class 'AxisSet3D'
perm_mat(x, ...)

# S4 method for class 'NeuroSpace'
perm_mat(x, ...)

Arguments

x: A NeuroSpace object
...: Additional arguments (not used)

Value

A numeric N x N matrix representing the permutation transform, where N is the dimensionality of the image.

A matrix representing the axis directions

A numeric N x N matrix representing the permutation transform, where N is the dimensionality of the image.

Details

a permutation matrix can be used to convert between cardinal image orientations. For example, if an image is stored in "RPI" (Right-Posterior-Inferior) format, a coordinate in this space can be converted to LPI (Left-Posterior-Inferior) by multiplying a coordinate vector by the permutation matrix.

Examples


fname <- system.file("extdata", "global_mask_v4.nii", package="neuroim2")
vol <- read_vol(fname)
pmat <- perm_mat(space(vol))

vox <- c(12,12,8)
pvox <- vox %*% perm_mat(space(vol))

stopifnot(all(pvox == c(-12,12,8)))