nii.qc.artefacts <- function(
img.nii, img.vol=1L,
air.nii, air.vol=1L, air.dir="eq", air.thresh=1,
save.dir, file.name) {
img <- read.nii.volume(img.nii, img.vol)
air <- read.nii.volume(air.nii, air.vol)
air <- thresh.apply(air,air.dir,air.thresh, "index.arr")
# find background threshold (mode excluding 0)
img[air] <- scale(img[air],
center = median(img[air]),
scale = mad(img[air]))
# threshold image
img <- img * (img > 0.1)
img <- (img > 10)*1
# open image, using mmand package
img <- opening(img, array(1, dim=c(3,3,3)))
# save artefact image
init.nii(file.name = paste0(save.dir, "/", file.name),
dims = dim(img),
pixdim = unlist(nii.hdr(img.nii, "pixim")),
orient = nii.orient(img.nii))
write.nii.volume(paste0(save.dir, "/", file.name), 1, img)
return(img)
}
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