afni_3dTshift: Convert AFNI File to NIFTI Image

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

Description

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

Usage

afni_3dTshift(file, tr, tpattern = c("alt+z", "alt+z2", "alt-z",
  "alt-z2", "seq+z", "seq-z"), tzero = NULL, slice = NULL,
  ignore_vols = 0, opts = "", retimg = TRUE, ...)

tshift(...)

Arguments

file	AFNI BRIK or HEAD file
tr	Repetition time. You may attach the suffix 's' for seconds, or 'ms' for milliseconds.
tpattern	Pattern of slice time pattern. alt+z = altplus = alternating in the plus direction alt+z2 = alternating, starting at slice #1 instead of #0 alt-z = altminus = alternating in the minus direction alt-z2 = alternating, starting at slice #nz-2 instead of #nz-1 seq+z = seqplus = sequential in the plus direction seq-z = seqminus = sequential in the minus direction
tzero	time offset to align each slice to (The default alignment time is the average of the 'tpattern' values)
slice	slice number indicating the time offset to align each slice to. If this is specified tzero may not be, and vice versa.
ignore_vols	Number of volumes to ignore/delete
opts	Additional options to pass to 3dTshift
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/afnir documentation built on May 22, 2021, 9:54 a.m.