[Mne_analysis] mne watershed_bem error, saving

[Kirill Elin]

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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:
>
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>
> 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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