run_fsl_command: Wrapper for running an FSL command safely within R

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

Wrapper for running an FSL command safely within R

Description

Wrapper for running an FSL command safely within R

Usage

run_fsl_command(
  args,
  fsldir = NULL,
  stdout = NULL,
  stderr = NULL,
  echo = TRUE,
  ...
)

Arguments

args	FSL command string to be run
fsldir	Location of FSL installation. If NULL, the function will search the environment for FSLDIR or FSL commands in the PATH
stdout	File target for redirecting stdout. If NULL, stdout will not be captured
stderr	File target for redirecting stderr. If NULL, stderr will not be captured
echo	Whether to print FSL command to the screen. Default: TRUE
...	Arguments passed through to the 'system' command.

Details

This command ensures that FSL command are run in an environment with FSL setup correctly.

Value

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

Author(s)

Michael Hallquist

Examples

## Not run: 
run_fsl_command("fslmaths test_data copy_data")

## End(Not run)

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