Mask image using FSL
This function calls fslmaths -mas to mask an image from
an image mask and either saves the image or returns an object of class nifti
fsl_mask(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE) fslmask(file, mask, outfile = NULL, retimg = TRUE, reorient = FALSE, intern = FALSE, opts = "", verbose = TRUE, ...)
... |
additional arguments passed to |
outfile |
(character) resultant masked image name |
retimg |
(logical) return image of class nifti |
file |
(character) image to be masked |
mask |
(character) mask given for image |
reorient |
(logical) If retimg, should file be reoriented when read in?
Passed to |
intern |
(logical) to be passed to |
opts |
(character) additional options to be passed to fslmask |
verbose |
(logical) print out command before running |
Result from system command, depends if intern is TRUE or FALSE.
Functions with underscores have different defaults and will return an output filename, so to be used for piping
if (have.fsl()){
system.time({
x = array(rnorm(1e5), dim = c(100, 100, 10))
img = nifti(x, dim= c(100, 100, 10),
datatype = convert.datatype()$FLOAT32, cal.min = min(x),
cal.max = max(x), pixdim = rep(1, 4))
mask = img > .5
masked = fslmask(img, mask = mask, retimg=TRUE)
})
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.