fsl_erode | R Documentation |
This function calls fslmaths -ero
to erode an image with either
the default FSL kernel or the kernel specified in kopts
. The function
either saves the image or returns an object of class nifti.
fsl_erode(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)
fslerode(
file,
outfile = NULL,
retimg = TRUE,
reorient = FALSE,
intern = FALSE,
kopts = "",
opts = "",
verbose = TRUE,
...
)
... |
additional arguments passed to |
outfile |
(character) resultant eroded image name |
retimg |
(logical) return image of class nifti |
file |
(character) image to be eroded |
reorient |
(logical) If retimg, should file be reoriented when read in?
Passed to |
intern |
(logical) to be passed to |
kopts |
(character) options for kernel |
opts |
(character) additional options to be passed to fslmaths |
verbose |
(logical) print out command before running |
Result from system command, depends if intern is TRUE or FALSE. If retimg is TRUE, then the image will be returned.
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)
})
}
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