Description Usage Arguments Value Author(s) Examples
View source: R/abpBrainExtraction.R
Brain extraction based on mapping a template image and its mask to the input image. Should be preceded by abpN4.
1 2 3 4 5 6 7 8 9 10 11 | abpBrainExtraction(
img,
tem,
temmask,
temregmask = NULL,
regtype = "SyN",
tdir = NA,
num_threads = 1,
pad = 0,
verbose = FALSE
)
|
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
|
pad |
argument passed to |
verbose |
print diagnostic messages |
outputs a brain image and brain mask.
Tustison N, Avants BB
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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)))
|
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