Threshold an image
This function calls fslmaths -thr -uthr to threshold an image
and either saves the image or returns an object of class nifti
fsl_thresh(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE) fslthresh(file, outfile = NULL, thresh = 0, uthresh = NULL, retimg = TRUE, reorient = FALSE, intern = FALSE, opts = "", verbose = TRUE, ...)
... |
additional arguments passed to |
outfile |
(character) name of resultant thresholded file |
retimg |
(logical) return image of class nifti |
file |
(character) filename of image to be thresholded |
thresh |
(numeric) threshold (anything below set to 0) |
uthresh |
(numeric) upper threshold (anything above set to 0) |
reorient |
(logical) If retimg, should file be reoriented when read in?
Passed to |
intern |
(logical) pass to |
opts |
(character) additional options to be passed to fslmaths |
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({
x = array(rnorm(1e6), dim = c(100, 100, 100))
img = nifti(x, dim= c(100, 100, 100),
datatype = convert.datatype()$FLOAT32, cal.min = min(x),
cal.max = max(x), pixdim = rep(1, 4))
thresh = fslthresh(img, thresh=0, uthresh = 2, retimg=TRUE)
})
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.