register_volume: Imaging registration using "NiftyReg"

In ravetools: Signal and Image Processing Toolbox for Analyzing Intracranial Electroencephalography Data

Imaging registration using 'NiftyReg'

Description

Registers 'CT' to 'MRI', or 'MRI' to another 'MRI'

Usage

register_volume(
  source,
  target,
  method = c("rigid", "affine", "nonlinear"),
  interpolation = c("cubic", "trilinear", "nearest"),
  threads = detect_threads(),
  symmetric = TRUE,
  verbose = TRUE,
  ...
)

Arguments

source	source imaging data, or a 'nifti' file path; for example, 'CT'
target	target imaging data to align to; for example, 'MRI'
method	method of transformation, choices are 'rigid', 'affine', or 'nonlinear'
interpolation	how volumes should be interpolated, choices are 'cubic', 'trilinear', or 'nearest'
threads, symmetric, verbose, ...	see niftyreg

Value

See niftyreg

Examples

source <- system.file("extdata", "epi_t2.nii.gz", package="RNiftyReg")
target <- system.file("extdata", "flash_t1.nii.gz", package="RNiftyReg")
aligned <- register_volume(source, target, verbose = FALSE)

source_img <- aligned$source[[1]]
target_img <- aligned$target
aligned_img <- aligned$image

oldpar <- par(mfrow = c(2, 2), mar = c(0.1, 0.1, 3.1, 0.1))

pal <- grDevices::grey.colors(256, alpha = 1)
image(source_img[,,30], asp = 1, axes = FALSE,
      col = pal, main = "Source image")
image(target_img[,,64], asp = 1, axes = FALSE,
      col = pal, main = "Target image")
image(aligned_img[,,64], asp = 1, axes = FALSE,
      col = pal, main = "Aligned image")

# bucket fill and calculate differences
aligned_img[is.nan(aligned_img) | aligned_img <= 1] <- 1
target_img[is.nan(target_img) | aligned_img <= 1] <- 1
diff <- abs(aligned_img / target_img - 1)
image(diff[,,64], asp = 1, axes = FALSE,
      col = pal, main = "Percentage Difference")

par(oldpar)

ravetools documentation built on Sept. 11, 2024, 9:06 p.m.