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<p>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...</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>De :</b> mne_analysis-bounces@nmr.mgh.harvard.edu <mne_analysis-bounces@nmr.mgh.harvard.edu> de la part de Eric Larson <larson.eric.d@gmail.com><br>
<b>Envoyé :</b> mardi 3 mars 2020 15:05:35<br>
<b>À :</b> Discussion and support forum for the users of MNE Software<br>
<b>Objet :</b> Re: [Mne_analysis] issue with mne watershed_bem</font>
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<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p>
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<div dir="ltr">... 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.
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<div>Eric</div>
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<div dir="ltr" class="gmail_attr">On Tue, Mar 3, 2020 at 10:03 AM Eric Larson <<a href="mailto:larson.eric.d@gmail.com">larson.eric.d@gmail.com</a>> wrote:<br>
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<div dir="ltr">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?
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<div>Eric</div>
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<div dir="ltr" class="gmail_attr">On Tue, Mar 3, 2020 at 9:56 AM Fleur GAUDFERNAU <<a href="mailto:fleur.gaudfernau@pasteur.fr" target="_blank">fleur.gaudfernau@pasteur.fr</a>> wrote:<br>
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<p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p>
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<p>Hello,</p>
<p>I am just getting started with MNE Python.</p>
<p>I have EEG and MRI data from a participant and I want to reconstruct the sources activity.</p>
<p>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 :</p>
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<p>(when calling </p>
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<p class="MsoNormal"><span lang="EN-US">$ mne watershed_bem --overwrite --subject=sub-0865_ses-01_isotrope --subjects-dir=subjects-dir)
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<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">Running mri_watershed for BEM segmentation with the following parameters:</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">Results dir = subjects-dir/sub-0865_ses-01_isotrope/bem/watershed</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">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</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">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</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">Mode:<span>
</span>use surfaceRAS to save surface vertex positions</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">Mode:<span>
</span>Saving out BEM surfaces</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">*********************************************************</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">The input file is subjects-dir/sub-0865_ses-01_isotrope/mri/T1.mgz</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">The output file is subjects-dir/sub-0865_ses-01_isotrope/bem/watershed/ws</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">mri_watershed Error: read failed</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"> </span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">mghRead(subjects-dir/sub-0865_ses-01_isotrope/mri/T1.mgz, -1): could not open file</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">('\nMode:<span>
</span>use surfaceRAS to save surface vertex positions\nMode:<span> </span>
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')</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">Traceback (most recent call last):</span></p>
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</span>File "/Users/XXX/anaconda3/bin/mne", line 11, in <module></span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"><span>
</span>load_entry_point('mne==0.20.dev0', 'console_scripts', 'mne')()</span></p>
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</span>File "/Users/XXX/anaconda3/lib/python3.7/site-packages/mne-0.20.dev0-py3.7.egg/mne/commands/utils.py", line 107, in main</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"><span>
</span>cmd.run()</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"><span>
</span>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</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"><span>
</span></span><span style="font-size:8pt;font-family:Courier">T1=T1, brainmask=brainmask, verbose=verbose)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier"><span>
</span></span><span style="font-size:8pt;font-family:Courier" lang="EN-US">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</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"><span>
</span>File "/Users/XXX/anaconda3/lib/python3.7/site-packages/mne-0.20.dev0-py3.7.egg/mne/utils/_logging.py", line 90, in wrapper</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"><span>
</span>return function(*args, **kwargs)</span></p>
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</span>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</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"><span>
</span>run_subprocess_env(cmd)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"><span>
</span>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</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"><span>
</span>File "/Users/XXX/anaconda3/lib/python3.7/site-packages/mne-0.20.dev0-py3.7.egg/mne/utils/_logging.py", line 90, in wrapper</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"><span>
</span>return function(*args, **kwargs)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"><span>
</span>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</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US"><span>
</span>raise subprocess.CalledProcessError(p.returncode, command, output)</span></p>
<p class="MsoNormal" style="margin-bottom:0.0001pt;line-height:normal"><span style="font-size:8pt;font-family:Courier" lang="EN-US">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.</span></p>
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<p>I do not understand why mne fails to read T1.mgz. The file should be correct.</p>
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<p>Thanks in advance !</p>
<p>Fleur Gaudfernau<br>
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