AFNI 3dAutomask function — afni

Wrapper for AFNI 3dAutomask function

afni_3dAutomask(file, mfrac = 0.5, gradual_clipping = TRUE,
  n_peels = 1, n_neighbors = 17, outfile = NULL, retimg = TRUE,
  opts = "", ...)

Automask(...)

automask(...)

Arguments

file	nifti object or NIfTI filename. If more than one is given, they are given names of the letters up to `z`.
mfrac	The 'clip level fraction', which must be a number between 0.1 and 0.9, which is passed to `afni_3dClipLevel`
gradual_clipping	The program uses a 'gradual' clip level by default, To use a fixed clip level, set `gradual_clipping = FALSE`.
n_peels	Peel the mask `n_peels` times, then unpeel. Designed to clip off protuberances less than 2*`n_peels` voxels thick.
n_neighbors	Define the number of neighbors needed for a voxel NOT to be peeled. The 18 nearest neighbors in the 3D lattice are used, so `n_neighbors` should be between 9 and 18.
outfile	Output filename, should have a `.nii.gz` extension
retimg	Should an image be returned (`TRUE`) or a filename?
opts	Additional options passed to `3dAutomask`
...	additional arguments to `afni_3dAFNItoNIFTI`

Value

Output filename of the brik