[Mne_analysis] issue with mne watershed_bem

Fleur GAUDFERNAU fleur.gaudfernau at pasteur.fr
Tue Mar 3 11:41:06 EST 2020
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I checked, it is not a path issue. Nor a permission one, I ran the command with the highest permission rights. And the other files in the directory were accessible when running other commands...



________________________________
De : mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> de la part de Eric Larson <larson.eric.d at gmail.com>
Envoyé : mardi 3 mars 2020 15:05:35
À : Discussion and support forum for the users of MNE Software
Objet : Re: [Mne_analysis] issue with mne watershed_bem


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... or actually perhaps it's a permissions issue. MNE already checks to make sure the file exists, but we don't for example check to see if it's readable by the user.

Eric


On Tue, Mar 3, 2020 at 10:03 AM Eric Larson <larson.eric.d at gmail.com<mailto:larson.eric.d at gmail.com>> wrote:
This looks like a path problem. Is your subjects-dir actually called "subjects-dir"? Does the file "subjects-dir/sub-0865_ses-01_isotrope/mri/T1.mgz" exist relative to the path from which you executed the `mne watershed_bem` command?

Eric


On Tue, Mar 3, 2020 at 9:56 AM Fleur GAUDFERNAU <fleur.gaudfernau at pasteur.fr<mailto:fleur.gaudfernau at pasteur.fr>> wrote:

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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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