[Mne_analysis] mne watershed_bem error, saving

[Bear, Joshua]

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Kirill / anyone else experiencing this issue: This problem appears to be fixed in the current master of the development version (thanks Eric for pointing this out!). Worked without a hitch on the subject I was having trouble with.

Thanks all,
Josh






On Feb 17, 2020, at 9:02 AM, Eric Larson <larson.eric.d at gmail.com<mailto:larson.eric.d at gmail.com>> wrote:


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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<mailto: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<mailto: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<mailto: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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