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)
iimg = 5
for (iimg in seq(nrow(df))) {
print(iimg)
ss_fname = df$ss[iimg]
mask_fname = df$mask[iimg]
img_fname = df$image[iimg]
label_fname = df$label[iimg]
if (!all(file.exists(ss_fname, mask_fname))) {
# aimg = antsImageRead(img_fname)
# # q25 = quantile(aimg[aimg > 0], probs = 0.25)
# q25 = 0
# mask = array(aimg > q25, dim = dim(aimg))
# mask = as.antsImage(mask, reference = aimg)
img = rpi_orient(img_fname)
img = img$img
label = rpi_orient(label_fname)
label = label$img
full_mask = img > 0
dd = dropEmptyImageDimensions(
full_mask,
other.imgs = list(img = img,
label = label))
img = dd$other.imgs$img
writenii(img, img_fname)
label = dd$other.imgs$label
writenii(label, label_fname)
mask = label > 0
filled = filler(mask, fill_size = 5) %>%
oMath("FillHoles")
filled = filled > 0
writenii(filled, mask_fname)
ss = mask_img(img, filled)
writenii(ss, ss_fname)
# ortho2(img, filled)
}
}
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