whitestripe: Performs White Stripe of T1 or T2 Images

In muschellij2/WhiteStripe: White Matter Normalization for Magnetic Resonance Images

Performs White Stripe of T1 or T2 Images

Description

Returns the mean/sd of the whitestripe and indices for them on the image

Usage

whitestripe(
  img,
  type = c("T1", "T2", "FA", "MD", "first", "last", "largest"),
  breaks = 2000,
  whitestripe.width = 0.05,
  whitestripe.width.l = whitestripe.width,
  whitestripe.width.u = whitestripe.width,
  arr.ind = FALSE,
  verbose = TRUE,
  stripped = FALSE,
  slices = NULL,
  ...
)

Arguments

img	Image (T1, T2, FA, or MD). Array or object of class nifti
type	T1, T2, FA, or MD image whitestripe
breaks	Number of breaks passed to hist
whitestripe.width	Radius of the white stripe
whitestripe.width.l	Lower Radius of the white stripe
whitestripe.width.u	Upper Radius of the white stripe
arr.ind	Whether indices should be array notation or not, passed to which
verbose	Print diagnostic information
stripped	Applying to skull-stripped image. NOTE: This does NOT do a subset of slices, as make_img_voi.
slices	slices to use for make_img_voi if only a subset to estimate the distribution.
...	Arguments to be passed to get.last.mode

Details

This function takes in an image and computes a window of the distribution called the white stripe. If you wish to pass in values you have subset, such as single from a skull-stripped image, you can pass in img and set the class to img_voi (class(img) = "img_voi") and this will not rerun make_img_voi.

Value

List of indices of whitestripe, last mode of histogram, array/nifti of 0/1 corresponding to the mask, mean of whitestripe, standard deviation of whitestripe

Examples

## Not run: 
library(WhiteStripe)
lib.loc = tempdir()
if (WhiteStripe::download_img_data(lib.loc = lib.loc)){
library(oro.nifti)
set.seed(1)
t1 = readNIfTI(system.file("T1Strip.nii.gz", package="WhiteStripe",
lib.loc = lib.loc))
t1.ind = whitestripe(t1, "T1")
set.seed(2)
t1_2 = readNIfTI(system.file("T1Strip.nii.gz", package="WhiteStripe",
lib.loc = lib.loc))
t1_2.ind = whitestripe(t1_2, "T1") 
t1.mask = whitestripe_ind_to_mask(t1, t1.ind$whitestripe.ind)
t1.mask[t1.mask == 0] = NA
orthographic(t1, t1.mask, col.y="red")
t2 = readNIfTI(system.file("T2Strip.nii.gz", package="WhiteStripe",
lib.loc = lib.loc))
t2.ind = whitestripe(t2, "T2")
t2.mask = whitestripe_ind_to_mask(t2, t2.ind$whitestripe.ind)
t2.mask[t2.mask == 0] = NA
orthographic(t2, t2.mask, col.y="red")
}

## End(Not run)

muschellij2/WhiteStripe documentation built on Aug. 31, 2022, 8:42 p.m.