nii.qc.cnr <- function(
img.nii, img.vol=1L,
gm.nii, gm.vol=1L, gm.dir="gt", gm.thresh=0,
wm.nii, wm.vol=1L, wm.dir="gt", wm.thresh=0,
air.nii, air.vol=1L, air.dir="eq", air.thresh=1) {
img <- read.nii.volume(img.nii, img.vol)
gm <- read.nii.volume(gm.nii, gm.vol)
gm <- thresh.apply(gm, gm.dir, gm.thresh, "index.arr")
wm <- read.nii.volume(wm.nii, wm.vol)
wm <- thresh.apply(wm, wm.dir, wm.thresh, "index.arr")
air <- read.nii.volume(air.nii, air.vol)
air <- thresh.apply(air, air.dir, air.thresh, "index.arr")
cnr <- abs(mean(img[gm]) - mean(img[wm]))/sqrt(sd(img[air])^2 + sd(img[gm])^2 + sd(img[wm])^2)
return(cnr)
}
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