run_afni_command: Wrapper for running an AFNI command safely within R

In UNCDEPENdLab/fmri.pipeline: Analysis of fMRI Data on HPC clusters

Wrapper for running an AFNI command safely within R

Description

Wrapper for running an AFNI command safely within R

Usage

run_afni_command(
  args,
  afnidir = NULL,
  stdout = NULL,
  stderr = NULL,
  echo = TRUE,
  omp_num_threads = 1L,
  ...
)

Arguments

args	AFNI command string to be run
afnidir	Location of AFNI installation. If NULL, the function will search the environment for AFNIDIR or afni on PATH
stdout	File target for redirecting stdout. If NULL, stdout will not be written to file.
stderr	File target for redirecting stderr. If NULL, stderr will not be written to file.
echo	Whether to print AFNI command to the screen. Default: TRUE
omp_num_threads	sets the number of OpenMP threads used for this AFNI command (if supported)
...	Arguments passed through to the 'system' command.

Details

This command ensures that AFNI commands are run in an environment that is setup correctly

Value

The exit status of the executed AFNI command. 0 for success, non-zero for failure

Author(s)

Michael Hallquist

Examples

## Not run: 
run_afni_command("3dcopy test_data copy_data")

## End(Not run)

UNCDEPENdLab/fmri.pipeline documentation built on April 3, 2025, 3:21 p.m.