Usage
susan(file, outfile = NULL, retimg = TRUE, reorient = FALSE, intern = FALSE, bthresh = 0.1, sigma = 3, dimg = c(3, 2), use_median = FALSE, n_usans = c(0, 1, 2), extra.scans = list(), opts = "", verbose = TRUE, ...)
Arguments
file
(character) image to be manipulated
outfile
(character) resultant image name (optional)
retimg
(logical) return image of class nifti
reorient
(logical) If retimg, should file be reoriented when read in?
Passed to readnii. intern
(logical) to be passed to system bthresh
brightness threshold and should be greater than noise level and less than contrast of edges to be preserved.
sigma
spatial size (sigma i.e. half-width) of smoothing in mm.
dimg
dimensionality (2 or 3) depending on whether smoothing is to be within-plane (2) or fully 3D (3).
use_median
determines whether to use a local median filter in the cases where single-point noise is detected (0 or 1).
n_usans
determines whether the smoothing area (USAN) is to be found from secondary images (0 1 or 2).
extra.scans
List of extra scans for USAN. List of
n_usans elements, where each element has 2 named objects
bthresh and filename
opts
(character) operations to be passed to susan, not
currently used.
verbose
(logical) print out command before running
...
additional arguments passed to fslcmd.