BUG: set_config() doesn't change value accessed via get_config()

It’s probably a bad setup on my part, but I can’t seem to make mne.bem.make_watershed_bem to work.

I try to explicitly export and source Freesurfer and MNE © in the bash and/or via subprocess or os.sys(), but I keep having the following error with the command

mne.bem.make_watershed_bem(subject, subjects_dir, overwrite=True)

Running mri_watershed for BEM segmentation with the following parameters:

SUBJECTS_DIR = /data/subjects
SUBJECT = hn120493
Results dir = /data/subjects/hn120493/bem/watershed

Running subprocess: mri_watershed -useSRAS -surf /data/subjects/hn120493/bem/watershed/hn120493 /data/subjects/hn120493/mri/T1.mgz /data/subjects/hn120493/bem/watershed/ws
Command not found: mri_watershed
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-5-f8d51723d992> in <module>()
----> 1 mne.bem.make_watershed_bem(subject, subjects_dir, overwrite=True)

/home/jrking/mne-python/mne/bem.pyc in make_watershed_bem(subject, subjects_dir, overwrite, volume, atlas, gcaatlas, preflood, show, verbose)

/home/jrking/mne-python/mne/utils.pyc in verbose(function, *args, **kwargs)
    627         with use_log_level(verbose_level):
    628             return function(*args, **kwargs)
--> 629     return function(*args, **kwargs)
    630 
    631 

/home/jrking/mne-python/mne/bem.pyc in make_watershed_bem(subject, subjects_dir, overwrite, volume, atlas, gcaatlas, preflood, show, verbose)
   1061                 'Results dir = %s\n' % (subjects_dir, subject, ws_dir))
   1062     os.makedirs(op.join(ws_dir, 'ws'))
-> 1063     run_subprocess(cmd, env=env, stdout=sys.stdout, stderr=sys.stderr)
   1064 
   1065     if op.isfile(T1_mgz):

/home/jrking/mne-python/mne/utils.pyc in run_subprocess(command, verbose, *args, **kwargs)

/home/jrking/mne-python/mne/utils.pyc in verbose(function, *args, **kwargs)
    627         with use_log_level(verbose_level):
    628             return function(*args, **kwargs)
--> 629     return function(*args, **kwargs)
    630 
    631 

/home/jrking/mne-python/mne/utils.pyc in run_subprocess(command, verbose, *args, **kwargs)
    930     logger.info("Running subprocess: %s" % ' '.join(command))
    931     try:
--> 932         p = subprocess.Popen(command, *args, **kwargs)
    933     except Exception:
    934         logger.error('Command not found: %s' % (command[0],))

/home/jrking/anaconda/lib/python2.7/subprocess.pyc in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags)
    708                                 p2cread, p2cwrite,
    709                                 c2pread, c2pwrite,
--> 710                                 errread, errwrite)
    711         except Exception:
    712             # Preserve original exception in case os.close raises.

/home/jrking/anaconda/lib/python2.7/subprocess.pyc in _execute_child(self, args, executable, preexec_fn, close_fds, cwd, env, universal_newlines, startupinfo, creationflags, shell, to_close, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite)
   1333                         raise
   1334                 child_exception = pickle.loads(data)
-> 1335                 raise child_exception
   1336 
   1337 

OSError: [Errno 2] No such file or directory

However, when running the command directly in the terminal it works fine mri_watershed -useSRAS -surf /data/subjects/hn120493/bem/watershed/hn120493 /data/subjects/hn120493/mri/T1.mgz /data/subjects/hn120493/bem/watershed/ws Command not found: mri_watershed.

I can’t get the pipeline to work though, because I am still missing the subject_surface file.

Any idea what I can do?.. Sorry for the noise.

[larsoner]

Try it with mri_watershed --version

[agramfort]

1. is fine with me