library(rtapas)
in_ci <- function() {
nzchar(Sys.getenv("CI"))
}
grid = 0.01
if (in_ci()) {
grid = 0.02
}
# Data is provided in the rtapas package as arrays. Below we will convert them to nifti objects.
# Create a list of gold standard manual segmentation
train_gold_standard_masks = list(gs1 = rtapas::gs1,
gs2 = rtapas::gs2,
gs3 = rtapas::gs3,
gs4 = rtapas::gs4,
gs5 = rtapas::gs5,
gs6 = rtapas::gs6,
gs7 = rtapas::gs7,
gs8 = rtapas::gs8,
gs9 = rtapas::gs9,
gs10 = rtapas::gs10)
# Convert the gold standard masks to nifti objects
train_gold_standard_masks = lapply(train_gold_standard_masks, oro.nifti::nifti)
# Make a list of the training probability maps
train_probability_maps = list(pmap1 = rtapas::pmap1,
pmap2 = rtapas::pmap2,
pmap3 = rtapas::pmap3,
pmap4 = rtapas::pmap4,
pmap5 = rtapas::pmap5,
pmap6 = rtapas::pmap6,
pmap7 = rtapas::pmap7,
pmap8 = rtapas::pmap8,
pmap9 = rtapas::pmap9,
pmap10 = rtapas::pmap10)
# Convert the probability maps to nifti objects
train_probability_maps = lapply(train_probability_maps, oro.nifti::nifti)
# Make a list of the brain masks
train_brain_masks = list(brain_mask1 = rtapas::brain_mask,
brain_mask2 = rtapas::brain_mask,
brain_mask3 = rtapas::brain_mask,
brain_mask4 = rtapas::brain_mask,
brain_mask5 = rtapas::brain_mask,
brain_mask6 = rtapas::brain_mask,
brain_mask7 = rtapas::brain_mask,
brain_mask8 = rtapas::brain_mask,
brain_mask9 = rtapas::brain_mask,
brain_mask10 = rtapas::brain_mask)
# Convert the brain masks to nifti objects
train_brain_masks = lapply(train_brain_masks, oro.nifti::nifti)
# Specify training IDs
train_ids = paste0('subject_', 1:length(train_gold_standard_masks))
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