This question is underspecified. You need to provide the whole output for context. I would suggest trying to run the commands from the command line instead of Python to troubleshoot the source of your error. Since modern file systems allow spaces in file paths, I would not use a space as a delimiter, rather provide your arguments as a list:

subprocess.call(["dcm2niix", "-z", "n", "-o", "~/outdir", "~/indir"])