fsl_fill | R Documentation |
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)
})
}
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