[Mne_analysis] mne watershed_bem error, saving

[Eric Larson]

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Can you open a GitHub issue with the full traceback? It's hopefully
something that we can fix.

Eric


On Fri, Feb 14, 2020 at 2:31 PM Kirill Elin <ekirling at gmail.com> wrote:

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>
> Dear Josh,
> 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.
> Best regards,
> Kirill
>
> пт, 14 февр. 2020 г. в 20:58, Bear, Joshua <JOSHUA.BEAR at cuanschutz.edu>:
>
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>>
>> 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.
>>
>> 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.
>>
>> Best,
>> Josh
>>
>>
>>
>>
>> Joshua Bear, MD, MA | Assistant Professor, Pediatric Neurology
>> and Epilepsy
>> University of Colorado and Children’s Hospital Colorado
>> 13123 East 16th Avenue, Box B-155 | Aurora, CO 80045 | Phone:
>> 720-777-6138 | Fax: 720-777-7285
>>
>> On Feb 14, 2020, at 11:52 AM, Kirill Elin <ekirling at gmail.com> wrote:
>>
>>         External Email - Use Caution
>>
>> Dear everybody,
>> I need to create BEM surfaces using the FreeSurfer watershed algorithm
>> for MEG data analysis using MNE-Python.
>> So I ran the command: mne watershed_bem --subject subjectname
>> And it runs e.g. till:
>> mri_watershed ru_nivcsw   12490
>> mri_watershed done
>> and quits with errors like:
>> (only final line are below)
>> 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
>>     raise IOError('Destination file exists. Please use option '
>> OSError: Destination file exists. Please use option "overwrite=True" to
>> force overwriting.
>>
>> Now, it is unclear what destination file is meant. This happens on
>> several machines
>> --overwrite option does not help at all.
>> 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.
>> FreeSurfer 6.0.0, Ubuntu, MNE 19.0.0
>> Thank you in advance.
>> Sincerely yours,
>> Kirill
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