ANTsR (version 1.0)

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, tdir = NA)

Arguments

img

image to which we map a brain mask

tem

Template image which has an associated label mask.

temmask

Template's antsImage brain mask.

tdir

temporary directory (optional)

Value

outputs a brain image and brain mask.

Examples

# NOT RUN {
fn<-getANTsRData("r16")
img<-antsImageRead(fn)
img<-resampleImage(img,c(128,128),1,0)
tf<-getANTsRData("r64")
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)
# }