Fill image holes
This function calls fslmaths -fillh to fill in image holes
and either saves the image or returns an object of class nifti
fsl_fill(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE) fslfill(file, outfile = NULL, bin = TRUE, retimg = TRUE, reorient = FALSE, intern = FALSE, verbose = TRUE, ...)
... |
additional arguments passed to |
outfile |
(character) name of resultant filled file |
retimg |
(logical) return image of class nifti |
file |
(character) filename of image to be filled |
bin |
(logical) binarize the image before filling |
reorient |
(logical) If retimg, should file be reoriented when read in?
Passed to |
intern |
(logical) pass to |
verbose |
(logical) print out command before running |
character or logical depending on intern
Functions with underscores have different defaults and will return an output filename, so to be used for piping
if (have.fsl()){
system.time({
dims = c(50, 50, 20)
x = array(rnorm(prod(dims)), dim = dims)
img = nifti(x, dim= dims,
datatype = convert.datatype()$FLOAT32, cal.min = min(x),
cal.max = max(x), pixdim = rep(1, 4))
mask = img > .5
eroded = fslerode(mask, kopts = "-kernel boxv 5", retimg=TRUE)
filled = fslfill(eroded, retimg= TRUE)
})
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.