abpBrainExtraction¶

purpose:

An ants-based brain extraction script.

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) )

examples:

# 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')

}

ANTsR 0.0.0 documentation

abpBrainExtraction

abpBrainExtraction¶