abpBrainExtraction: An ants-based brain extraction script.

In stnava/itkImageR: Examples using Rcpp to interface R and ITK

Description

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

Usage

abpBrainExtraction( img=imgToBExtract, tem = template, temmask = mask, tempriors=c(img1,img2,...,imgN) )

Arguments

img	image to which we map a brain mask
tem	Template image which has an associated label mask.
tmask	Template's antsImage brain mask.
tempriors=c(img1,img2,...,imgN)	Vector of spatial priors - NOT IMPLEMENTED YET

Value

outputs a brain image and brain mask. 1 – Failure

Author(s)

Tustison N, Avants BB

Examples

## Not run: 
# short example first
fn<-getANTsRData('r16')
img<-antsImageRead(fn,2)
tf<-getANTsRData('r64')
tem<-antsImageRead(tf,2)
temmask<-antsImageClone( tem )
temmask[ tem  > 20 ]<-1 
temmask[ tem  <= 20 ]<-0 
bm<-abpBrainExtraction(img=img,tem=tem,temmask=temmask)

# more complete example
idim<-2
fn<-getANTsRData('r16')
img<-antsImageRead(fn,idim)
tf<-getANTsRData('r64')
atem<-antsImageRead(tf,idim)
temmask<-antsImageClone( atem )
temmask[ atem > 20 ]<-1
temmask[ atem <= 20 ]<-0
tsegs <- Atropos(d = idim, a = atem, m = "[0.2,1x1]", c = "[5,0]", i ="kmeans[3]", x = temmask)
acsf<-tsegs$probabilityimages[[1]]
agm<-tsegs$probabilityimages[[2]]
awm<-tsegs$probabilityimages[[3]]
abm<-temmask
kk<-abpN4(img)
kkbm<-abpBrainExtraction(img=kk,tem=atem,temmask=abm)
kcsf<-antsApplyTransforms(fixed=kk,moving=acsf,transformlist=kkbm$invtransforms)
kgm<-antsApplyTransforms(fixed=kk,moving=agm,transformlist=kkbm$invtransforms)
kwm<-antsApplyTransforms(fixed=kk,moving=awm,transformlist=kkbm$invtransforms)
plotANTsImage(kk,slices='40x120x20',functional=kwm,thresh='0.5x1')
for ( its in 1:3 ) {
  kk<-abpN4( img , weight = kwm , mask = kkbm$bmask )
  ksegs <- Atropos(d = kk@dimension, a = kk, m = "[0.1,1x1]", c = "[5,0]",
    i = list( kcsf, kgm, kwm) , x = kkbm$bmask )
  kcsf<-ksegs$probabilityimages[[1]]
  kgm<-ksegs$probabilityimages[[2]]
  kwm<-ksegs$probabilityimages[[3]]
  plotANTsImage(kk,slices='40x120x20',functional=kwm,thresh='0.5x1')
}


## End(Not run)

stnava/itkImageR documentation built on May 30, 2019, 7:21 p.m.