afni_3dAutomask: AFNI 3dAutomask function

In muschellij2/afnir: Wrapper Functions for 'AFNI' (Analysis of Functional 'NeuroImages')

Description

Wrapper for AFNI 3dAutomask function

Usage

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

muschellij2/afnir documentation built on May 23, 2019, 8:33 a.m.