subprocess env is not set properly

[kingjr]

While running mne.bem.mne_make_watershed_bem I ran into a unspecific error:
Error: io.UnsupportedOperation: fileno

which is due to a subprocess error triggered earlier ('mri_watershed not found').

I tried changing FREESURFER_HOME via mne.set_config without luck.

I manually changed run_subprocess, as follow, which fixed the issue.

def run_subprocess(command, return_code=False, verbose=None, *args, **kwargs):    
    import subprocess, os
    my_env = os.environ.copy()
    my_env["PATH"] = "/usr/sbin:/sbin:" + my_env["PATH"]

    cp = subprocess.run(command, 
                        env=my_env,
                        universal_newlines=True, 
                        stdout=subprocess.PIPE, 
                        stderr=subprocess.PIPE)
    return cp.stdout, cp.stderr

(And if someone opens a PR, you can pass the missing overwrite param here https://github.com/mne-tools/mne-python/blob/master/mne/bem.py#L1156)

[agramfort]

you hacked the path? this function looks very different from https://github.com/mne-tools/mne-python/blob/master/mne/utils/misc.py#L85 are you using latest release/master?

[kingjr]

you hacked the path?

In the fix yes, else no.

this function looks very different from

Yes, I went for the simplest possible fix ;)

This solved the issue for me, but I don't want to open a PR, because it's not a pure-python, platform-independent, easy-to-debug issue.

are you using latest release/master?

yes

[agramfort]

@larsoner any thought? It's hard to integrate a fix like this unless we can replicate...

…

[larsoner]

#6991 should fix it. Either use that branch, or export FREESURFER_HOME=... in your terminal before starting the Python interpreter (which is probably what most folks do, which is why nobody hit/reported this yet).

[kingjr]

FWIW, I did export FREESURFER_HOME prior to python interpreter.

#6991 seems to works fine