FSL SUSAN noise reduction — susan • fslr

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

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`.

Value

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

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.