afni Command Wrapper — afni

This function calls AFNI command passed to func

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.