An ants-based brain extraction script.

Brain extraction based on mapping a template image and its mask to the input image. Should be preceded by abpN4.

abpBrainExtraction(
  img,
  tem,
  temmask,
  temregmask = NULL,
  regtype = "SyN",
  tdir = NA,
  num_threads = 1,
  pad = 0,
  verbose = FALSE
)

Arguments

img	whole head image to which we map a brain mask
tem	Template image (the whole head) which has an associated label mask.
temmask	Template's antsImage brain mask.
temregmask	Template's registration mask including skull but not the face
regtype	registration type: 'SyN' (fast, default), 'SyNabp' (better, slower)
tdir	temporary directory (optional)
num_threads	will execute Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = num_threads) before running to attempt a more reproducible result. See https://github.com/ANTsX/ANTs/wiki/antsRegistration-reproducibility-issues for discussion. If NULL, will not set anything.
pad	argument passed to iMath for how much to zero-pad the image
verbose	print diagnostic messages

Value

outputs a brain image and brain mask.

Author

Tustison N, Avants BB

Examples

Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = 1)
set.seed(1)
n = 64
fn<-getANTsRData("r16")
img<-antsImageRead(fn)
img<-resampleImage(img,c(n,n),1,0)
tf<-getANTsRData("r27")
tem<-antsImageRead(tf)
tem<-resampleImage(tem,c(n,n),1,0)
temmask<-antsImageClone( tem )
temmask[ tem  > 20 ] <- 1
temmask[ tem  <= 20 ] <- 0
bm<-ANTsR::abpBrainExtraction(img=img,tem=tem,temmask=temmask, num_threads = 1)
stopifnot(sum(bm$bmask) != prod(dim(bm$brain)))
bm2<-ANTsR::abpBrainExtraction(img=img,tem=tem,temmask=temmask, num_threads = 1)
stopifnot(sum(bm2$bmask) != prod(dim(bm2$brain)))