susan: FSL SUSAN noise reduction

In muschellij2/fslr: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

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,
  ...
)

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.

muschellij2/fslr documentation built on May 10, 2024, 2:12 a.m.