Description Usage Arguments Value Examples
Removes the neck from axially acquired scan so skull stripping can be done.
1 2 3 |
file |
File for neck removal - either filename or class nifti |
template.file |
Template to warp to original image space |
template.mask |
Mask of template to use as rough brain mask. If
|
ret_mask |
Return mask of slices to keep |
typeofTransform |
Transformation for template to image, passed to
|
rep.value |
Value to replace neck slices with |
swapdim |
Should the dimensions be swapped before registration, and then reset after |
verbose |
Print out diagnostic messages |
... |
Additional arguments passed to |
Object of class nifti or vector of indices
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | if (fslr::have.fsl()){
print(fslr::fsl_version())
in_ci <- function() {
nzchar(Sys.getenv("CI"))
}
if (in_ci()) {
destfile = tempfile(fileext = ".nii.gz")
dl = download.file(paste0(
"https://github.com/muschellij2/",
"Neurohacking/files/3454385/113-01-MPRAGE2.nii.gz"),
destfile = destfile)
tfile = fslr::mni_fname(brain = TRUE)
if (file.exists(tfile)) {
res = remove_neck(
destfile,
template.file = tfile,
template.mask = fslr::mni_fname(brain = TRUE, mask = TRUE)
)
}
}
}
|
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