afni_3dDespike: Convert AFNI File to NIFTI Image

In neuroconductor-devel-releases/afnir: Wrapper Functions for 'AFNI' (Analysis of Functional 'NeuroImages')

Description

Converts an AFNI file to an NIfTI file or nifti using 3dDespike

Usage

afni_3dDespike(file, ignore_vols = 0, curve_order = NULL,
  cut_values = c(2.5, 4), mask = TRUE, dilate = 4,
  localedit = FALSE, method = c("OLD", "NEW"), opts = "",
  retimg = TRUE, ...)

despike(...)

Arguments

file	AFNI BRIK or HEAD file
ignore_vols	Number of volumes to ignore/delete
curve_order	the curve fit order
cut_values	a length 2 vector with the first being the threshold value of sigma for a spike and the second being the upper range of the allowed deviation from the curve:
mask	should a mask of high-intensity voxels be used (TRUE) or all voxels (FALSE)
dilate	dilation factor of the mask
localedit	Change the editing process to the following: If a voxel |s| value is >= c2, then replace the voxel value with the average of the two nearest non-spike (|s| < c2) values; the first one previous and the first one after. Note that the first cut value is not used here.
method	should the NEW or OLD method be used for the L1 fit. NEW is faster
opts	Additional options to pass to 3dDespike
retimg	Should an image be returned?
...	additional arguments to readnii

Value

If retimg then object of class nifti. Otherwise, the outfile argument is returned (or a temporary filename)

neuroconductor-devel-releases/afnir documentation built on May 6, 2020, 3:22 p.m.