[Mne_analysis] issue with mne watershed_bem

[Fleur GAUDFERNAU]

        External Email - Use Caution        

Hello,

I am just getting started with MNE Python.

I have EEG and MRI data from a participant and I want to reconstruct the sources activity.

I do not have the surfaces necessary to make the bem model (ie inner skull, outer skin and outer skull). Hence I used mne_watershed_bem to create the bem surfaces. At this point, I get the following error :


(when calling
$ mne watershed_bem --overwrite --subject=sub-0865_ses-01_isotrope --subjects-dir=subjects-dir)

Running mri_watershed for BEM segmentation with the following parameters:
Results dir = subjects-dir/sub-0865_ses-01_isotrope/bem/watershed
Command = mri_watershed -useSRAS -surf subjects-dir/sub-0865_ses-01_isotrope/bem/watershed/sub-0865_ses-01_isotrope subjects-dir/sub-0865_ses-01_isotrope/mri/T1.mgz subjects-dir/sub-0865_ses-01_isotrope/bem/watershed/ws
Running subprocess: mri_watershed -useSRAS -surf subjects-dir/sub-0865_ses-01_isotrope/bem/watershed/sub-0865_ses-01_isotrope subjects-dir/sub-0865_ses-01_isotrope/mri/T1.mgz subjects-dir/sub-0865_ses-01_isotrope/bem/watershed/ws

Mode:          use surfaceRAS to save surface vertex positions
Mode:          Saving out BEM surfaces

*********************************************************

The input file is subjects-dir/sub-0865_ses-01_isotrope/mri/T1.mgz
The output file is subjects-dir/sub-0865_ses-01_isotrope/bem/watershed/ws

mri_watershed Error: read failed

mghRead(subjects-dir/sub-0865_ses-01_isotrope/mri/T1.mgz, -1): could not open file
('\nMode:          use surfaceRAS to save surface vertex positions\nMode:          Saving out BEM surfaces\n\n*********************************************************\nThe input file is subjects-dir/sub-0865_ses-01_isotrope/mri/T1.mgz\nThe output file is subjects-dir/sub-0865_ses-01_isotrope/bem/watershed/ws\n\nmri_watershed Error: read failed\n\n', 'mghRead(subjects-dir/sub-0865_ses-01_isotrope/mri/T1.mgz, -1): could not open file\n')
Traceback (most recent call last):
  File "/Users/XXX/anaconda3/bin/mne", line 11, in <module>
    load_entry_point('mne==0.20.dev0', 'console_scripts', 'mne')()
  File "/Users/XXX/anaconda3/lib/python3.7/site-packages/mne-0.20.dev0-py3.7.egg/mne/commands/utils.py", line 107, in main
    cmd.run()
  File "/Users/XXX/anaconda3/lib/python3.7/site-packages/mne-0.20.dev0-py3.7.egg/mne/commands/mne_watershed_bem.py", line 82, in run
    T1=T1, brainmask=brainmask, verbose=verbose)
  File "</Users/XXX/anaconda3/lib/python3.7/site-packages/mne-0.20.dev0-py3.7.egg/mne/externals/decorator.py:decorator-gen-50>", line 2, in make_watershed_bem
  File "/Users/XXX/anaconda3/lib/python3.7/site-packages/mne-0.20.dev0-py3.7.egg/mne/utils/_logging.py", line 90, in wrapper
    return function(*args, **kwargs)
  File "/Users/XXX/anaconda3/lib/python3.7/site-packages/mne-0.20.dev0-py3.7.egg/mne/bem.py", line 1150, in make_watershed_bem
    run_subprocess_env(cmd)
  File "</Users/XXX/anaconda3/lib/python3.7/site-packages/mne-0.20.dev0-py3.7.egg/mne/externals/decorator.py:decorator-gen-1>", line 2, in run_subprocess
  File "/Users/XXX/anaconda3/lib/python3.7/site-packages/mne-0.20.dev0-py3.7.egg/mne/utils/_logging.py", line 90, in wrapper
    return function(*args, **kwargs)
  File "/Users/XXX/anaconda3/lib/python3.7/site-packages/mne-0.20.dev0-py3.7.egg/mne/utils/misc.py", line 163, in run_subprocess
    raise subprocess.CalledProcessError(p.returncode, command, output)
subprocess.CalledProcessError: Command '['mri_watershed', '-useSRAS', '-surf', 'subjects-dir/sub-0865_ses-01_isotrope/bem/watershed/sub-0865_ses-01_isotrope', 'subjects-dir/sub-0865_ses-01_isotrope/mri/T1.mgz', 'subjects-dir/sub-0865_ses-01_isotrope/bem/watershed/ws']' returned non-zero exit status 1.


I do not understand why mne fails to read T1.mgz. The file should be correct.


Thanks in advance !

Fleur Gaudfernau
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