rm(list = ls())
library(neurobase)
library(extrantsr)
library(ANTsR)
library(fslr)
imgs = list.files(pattern = "\\d.nii.gz")
df = data.frame(image = imgs,
label = gsub("[.]nii", "_glm.nii", imgs),
stringsAsFactors = FALSE)
df$ss = gsub("[.]nii", "_SS.nii", df$image)
df$mask = gsub("[.]nii", "_mask.nii", df$image)
df$fast = gsub("[.]nii", "_tissues.nii", df$image)
iimg = 1
for (iimg in seq(nrow(df))) {
print(iimg)
img_fname = df$image[iimg]
ss_fname = df$ss[iimg]
mask_fname = df$mask[iimg]
label_fname = df$fast[iimg]
if (!all(file.exists(label_fname))) {
ss = readnii(ss_fname)
mask = readnii(mask_fname)
# qimg = quantile_img(ss, mask = mask)
ss = robust_window(ss, mask = mask,
probs = c(0, 0.9999))
ss = mask_img(ss, mask)
bc = bias_correct(ss,
mask = mask_fname,
convergence = list(
iters = rep(400, 4),
tol = 1e-07),
correction = "N4")
tissues = fast(bc, bias_correct = FALSE)
writenii(tissues, filename = label_fname)
# ortho2(img, filled)
}
}
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