susan: FSL SUSAN noise reduction

Description

Implements Smallest Univalue Segment Assimilating Nucleus (SUSAN) noise reduction technique from FSL

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,
  ...
)

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

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.

References

S.M. Smith and J.M. Brady. SUSAN -a new approach to low level image processing. International Journal of Computer Vision, 23(1):45-78, May 1997.