mne watershed_bem error, saving

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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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2

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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

3

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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

??, 14 ???. 2020 ?. ? 20:58, Bear, Joshua <JOSHUA.BEAR at cuanschutz.edu>:

        External Email - Use Caution

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

        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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4

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

Eric

5

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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