Compute cortical thickness using the DiReCT algorithm.

Diffeomorphic registration-based cortical thickness based on probabilistic segmentation of an image. This is an optimization algorithm.

kellyKapowski(
  s,
  g,
  w,
  its = 45,
  r = 0.025,
  m = 1.5,
  x = FALSE,
  e = FALSE,
  q = NULL,
  timeSigma = 1,
  verbose = FALSE,
  ...
)

Arguments

s

segmentation image

g

gray matter probability image

w

white matter probability image

its

convergence params - controls iterations

r

gradient descent update parameter

m

gradient field smoothing parameter

x

matrix-based smoothing

e

restrict deformation boolean

q

time spacing, a vector equal to the number of time dimensions

timeSigma,

a scalar sigma value for distances between time points

verbose

boolean

...

anything else, see KK help in ANTs

Value

thickness antsImage

Author

Shrinidhi KL, Avants BB

Examples

img <- antsImageRead(getANTsRData("r16"), 2)
img <- resampleImage(img, c(64, 64), 1, 0)
mask <- getMask(img)
segs <- kmeansSegmentation(img, k = 3, kmask = mask)
thk <- kellyKapowski(
  s = segs$segmentation, g = segs$probabilityimages[[2]],
  w = segs$probabilityimages[[3]], its = 45, r = 0.5, m = 1
)