ANTsR (version 0.3.3)

abpBrainExtraction: 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 = NA, tem = NA, temmask = NA, temregmask = NA, regtype = "SyN", tdir = NA)

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)

Value

outputs a brain image and brain mask.

Examples

fn<-getANTsRData("r16")
img<-antsImageRead(fn)
img<-resampleImage(img,c(128,128),1,0)
tf<-getANTsRData("r27")
tem<-antsImageRead(tf)
tem<-resampleImage(tem,c(128,128),1,0)
temmask<-antsImageClone( tem )
temmask[ tem  > 20 ]<-1
temmask[ tem  <= 20 ]<-0
bm<-abpBrainExtraction(img=img,tem=tem,temmask=temmask)