zscore_img: Get Z-score over a margin of an img

In neuroconductor/neurobase: 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects

Description

Standardizes an image either by the axial, sagittal, or coronal slice or whole image

Usage

zscore_img(
  img,
  mask = NULL,
  margin = NULL,
  centrality = c("mean", "median", "trimmed_mean"),
  variability = c("sd", "iqrdiff", "mad", "maddiff", "iqr", "trimmed_sd"),
  trim = 0.2,
  remove.na = TRUE,
  remove.nan = TRUE,
  remove.inf = TRUE,
  remove.val = 0,
  remask = TRUE
)

Arguments

img	character path of image or an object of class nifti
mask	character path of mask or an object of class nifti
margin	Margin of image to z-score over (NULL - whole brain, 3-Axial, 2-Sagittal, 1-Coronal)
centrality	(character) Measure to center the data, either mean or median
variability	(character) Measure to scale the data
trim	if centrality is trimmed_mean or variability is trimmed_sd, then the amount of trimming
remove.na	(logical) change NAs to remove.val
remove.nan	(logical) change NaN to remove.val
remove.inf	(logical) change Inf to remove.val
remove.val	(logical) value to put the NA/NaN/Inf
remask	(logical) Should the image be remasked after normalizing?

Value

Array of object of class nifti

See Also

aperm

Examples

dim = c(100, 30, 5)
img = array(rnorm(prod(dim), mean=4, sd=4), 
dim=dim)

truth2 = img
for (i in 1:dim(img)[2]) {
truth2[,i,] = (truth2[,i,]- mean(truth2[,i,]))/sd(truth2[,i,])
}

truth1 = img
for (i in 1:dim(img)[1]) {
truth1[i,,] = (truth1[i,,]- mean(truth1[i,,]))/sd(truth1[i,,])
}

truth3 = img
for (i in 1:dim(img)[3]) {
truth3[,,i] = (truth3[,,i]- mean(truth3[,,i]))/sd(truth3[,,i])
}
try3 = zscore_img(img, margin=3)
stopifnot(all.equal(try3, truth3))
try2 = zscore_img(img, margin=2)
stopifnot(all.equal(try2, truth2))
try1 = zscore_img(img, margin=1)
stopifnot(all.equal(try1, truth1))
  
z = zscore_img(img, margin=NULL)
ztrim = zscore_img(img, margin=NULL, 
centrality = "trimmed_mean", variability = "trimmed_sd")

z = zscore_img(img, centrality = "median", variability = "iqr")
z = zscore_img(img, centrality = "median", variability = "iqrdiff")
z = zscore_img(img, centrality = "median", variability = "maddiff")

neuroconductor/neurobase documentation built on May 19, 2021, 5:24 a.m.