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<p>Hello,</p>
<p>We tried what you suggested.</p>
<p>mri_converts is working just fine on the file.</p>
<p>We ran the last mne version (v0.20dev0) and the error remains the same.<br>
</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 16:45:54<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>
<p></p>
<div dir="ltr">Are you able to read it using Freesurfer commands like:
<div><br>
</div>
<div><span style="color:rgb(0,0,0);font-family:Courier;font-size:10.6667px">mri_convert subjects-dir/sub-</span><span style="color:rgb(0,0,0);font-family:Courier;font-size:10.6667px">0865_ses-01_isotrope/mri/T1.</span><span style="color:rgb(0,0,0);font-family:Courier;font-size:10.6667px">mgz
~/test.nii</span><br>
</div>
<div><span style="color:rgb(0,0,0);font-family:Courier;font-size:10.6667px"><br>
</span></div>
This should at least verify that Freesurfer can read your file. But really this is all that MNE should be trying to do. You could then try changing over to the branch from this PR to see if it flags anything as being wrong:
<div><br>
</div>
<div><a href="https://github.com/mne-tools/mne-python/pull/7370">https://github.com/mne-tools/mne-python/pull/7370</a><br>
</div>
<div><br>
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<div>We can also iterate there until we figure it out.</div>
<div><br>
</div>
<div>Eric</div>
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</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Mar 3, 2020 at 11:41 AM Fleur GAUDFERNAU <<a href="mailto:fleur.gaudfernau@pasteur.fr">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>
<p></p>
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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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</p>
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<hr style="display:inline-block;width:98%">
<div id="gmail-m_-8320896509127860266divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>De :</b>
<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a> <<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a>> de la part de Eric
Larson <<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@gmail.com</a>><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>
<div> </div>
</div>
<div>
<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>
<p></p>
<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.
<div><br>
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<div>Eric</div>
<div><br>
</div>
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<div class="gmail_quote">
<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" target="_blank">larson.eric.d@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<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?
<div><br>
</div>
<div>Eric</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<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>
</div>
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<div dir="ltr">
<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>
<p></p>
<div id="gmail-m_-8320896509127860266gmail-m_-1163530357331873403gmail-m_4965153805067027958divtagdefaultwrapper" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif" dir="ltr">
<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>
<p><br>
</p>
<p>(when calling </p>
<div>
<p class="MsoNormal"><span lang="EN-US">$ mne watershed_bem --overwrite --subject=sub-0865_ses-01_isotrope --subjects-dir=subjects-dir)
<br>
</span></p>
<p class="MsoNormal"><span lang="EN-US"><br>
</span></p>
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<p></p>
<p></p>
<div>
<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>
<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/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>
<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/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>
<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/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></p>
<p><br>
</p>
<p>I do not understand why mne fails to read T1.mgz. The file should be correct.</p>
<p><br>
</p>
<p>Thanks in advance !</p>
<p>Fleur Gaudfernau<br>
</p>
</div>
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