dropEmptyImageDimensions {neurobase}

Drop Empty Image Dimensions

Description

Drops dimensions of an image that has all irrelevant values

Usage

dropEmptyImageDimensions(
  img,
  value = 0,
  threshold = 0,
  other.imgs = NULL,
  keep_ind = FALSE,
  reorient = FALSE
)

drop_empty_dim(
  img,
  value = 0,
  threshold = 0,
  other.imgs = NULL,
  keep_ind = FALSE,
  reorient = FALSE
)

Arguments

img

nifti object

value

Value to check against. If zero, then dropEmptyImageDimensions will drop any dimension that has fewer than threshold zeroes. May be a vector of values, matched with match

threshold

Drop dimension if fewer than threshold voxels are in the slice

other.imgs

List of other nifti objects or filenames to apply the same dropping as img.

keep_ind

keep indices in output. Will return list, even if other.imgs not specified

reorient

Should image be reoriented if a filename?

Value

List of output image indices, and other images if other.imgs not specified or keep_ind = TRUE. Otherwise object of class nifti

Note

drop_empty_dim is a shorthand for dropEmptyImageDimensions with all the same arguments. Also, NA are set to zero.

See Also

getEmptyImageDimensions

Examples

set.seed(5)
dims = rep(10, 3)
arr = array(rnorm(prod(dims)), dim = dims)
arr[,,10] = 0
nim = oro.nifti::nifti(arr)

dnim = dropEmptyImageDimensions(nim, keep_ind = TRUE)
new_nim = dnim$outimg
names(dnim)
dnim = dropEmptyImageDimensions(nim, keep_ind = TRUE, other.imgs = nim)
dims = rep(10, 4)
arr = array(rnorm(prod(dims)), dim = dims)
nim = oro.nifti::nifti(arr)

testthat::expect_error(
{dnim = dropEmptyImageDimensions(nim, keep_ind = TRUE)}
)