perm_mat-methods: Extract permutation matrix associated with an image

In bbuchsbaum/neuroim2: Data Structures and IO for Neuroimaging Data with an Emphasis on Functional Magnetic Resonance Imaging (FMRI)

Extract permutation matrix associated with an image

Description

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

Usage

perm_mat(x, ...)

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

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

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

Arguments

x	the object
...	additional arguments

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.

Value

an N x N permutation matrix, where N is the dimensionality of the image.

Examples

fname <- system.file("extdata", "global_mask.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)))

bbuchsbaum/neuroim2 documentation built on June 4, 2024, 11:23 p.m.