afni_cmd: afni Command Wrapper

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

Description

This function calls AFNI command passed to func

Usage

afni_cmd(func, file, outfile = NULL, retimg = TRUE, reorient = FALSE,
  intern = FALSE, opts = "", verbose = TRUE, samefile = FALSE,
  opts_after_outfile = FALSE, frontopts = "", add_ext = TRUE,
  bin_app = "bin", quote_file = TRUE, quote_outfile = TRUE,
  run = TRUE, ...)

Arguments

func	(character) AFNI function
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
opts	(character) operations to be passed to func
verbose	(logical) print out command before running
samefile	(logical) is the output the same file?
opts_after_outfile	(logical) should opts come after the outfile in the AFNI command?
frontopts	(character) options/character to put in before filename
add_ext	(logical) should the extension be added to the outfile
bin_app	(character) appendix to add to get_afni
quote_file	should the filename be quoted in double quotes?
quote_outfile	should the output filename be quoted in double quotes?
run	(logical) Should the command be run? If this is false, nothing is done
...	additional arguments passed to system.

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.

neuroconductor/afnir documentation built on May 22, 2021, 9:54 a.m.