This function takes a slice object and first applies a filter with default settings to the image set as the slice registration path. An interative user loop allows for easy adjustment of the brain threshold since the wholebrain GUI tends to be a bit buggy. This function then returns a filter with the adjusted brain threshold.
Arguments
- s
slice object
- filter
(list, default = NULL) If the user passes their own filter list, it will use that instead of the presaved filter list from SMARTTR.
Examples
if (FALSE) {
# Adjust the brain threshold, then run register on the slice object
filter <- adjust_brain_outline(s); s <- register(s, filter = filter)
}