<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"><div>Dear Josh,</div><div>Miraculously it worked for one subject of mine on one of the machines. I redid segmentation on two machines of other subjects to no avail. Also, do not understand what the difference is.</div><div>Best regards,</div><div>Kirill<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">пт, 14 февр. 2020 г. в 20:58, Bear, Joshua <<a href="mailto:JOSHUA.BEAR@cuanschutz.edu">JOSHUA.BEAR@cuanschutz.edu</a>>:<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 style="overflow-wrap: break-word;"><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>
For what it’s worth, I just ran across this problem with one of my subjects as well. I had no issues with another subject, and haven’t pinpointed the difference yet. I’m also re-running the Freesurfer segmentation now to see if something got changed along the
way.
<div><br>
</div>
<div>If no one has a definitive answer, I’ll keep digging on possible differences in the study subjects that could identify the problem and open an issue on GitHub. </div>
<div><br>
</div>
<div>Best,</div>
<div>Josh</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
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<div><br>
<div>
<div>Joshua Bear, MD, MA | Assistant Professor, Pediatric Neurology and Epilepsy<br>
University of Colorado and Children’s Hospital Colorado<br>
13123 East 16th Avenue, Box B-155 | Aurora, CO 80045 | Phone: 720-777-6138 | Fax: 720-777-7285 </div>
</div>
<div><br>
<blockquote type="cite">
<div>On Feb 14, 2020, at 11:52 AM, Kirill Elin <<a href="mailto:ekirling@gmail.com" target="_blank">ekirling@gmail.com</a>> wrote:</div>
<br>
<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>
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<div>Dear everybody,<br>
</div>
I need to create BEM surfaces using the FreeSurfer watershed algorithm for MEG data analysis using MNE-Python.
<div>So I ran the command: mne watershed_bem --subject subjectname <br>
</div>
<div>And it runs e.g. till:<br>
</div>
<div>mri_watershed ru_nivcsw 12490<br>
mri_watershed done</div>
<div>and quits with errors like:</div>
<div>(only final line are below)<br>
</div>
<div>File "/work/modules/Ubuntu/14.04/amd64/common/anaconda3/latest/envs/neuroimaging/lib/python3.6/site-packages/mne/utils/check.py", line 143, in _check_fname<br>
raise IOError('Destination file exists. Please use option '<br>
OSError: Destination file exists. Please use option "overwrite=True" to force overwriting.</div>
<div><br>
</div>
<div>Now, it is unclear what destination file is meant. This happens on several machines
<br>
</div>
<div>--overwrite option does not help at all.</div>
<div>The correct outcome should include bem folder with resulting files and also watershed subfolder with resulting files. In case of the error above the files in bem folder are missing and there are files only in watershed subfolder.</div>
<div>FreeSurfer 6.0.0, Ubuntu, MNE 19.0.0 <br>
</div>
<div>Thank you in advance.</div>
<div>Sincerely yours,</div>
<div>Kirill</div>
</div>
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