[Mne_analysis] Creating bem meshes with mne_watershed_bem - mne_convert_surface not found

[Alexandre Gramfort]

.the rest of the script requires freesurfer but here you miss an MNE
Unix command called mne_convert_surface.

make sure you have installed

freesurfer
mne-python
mne

See:

http://martinos.org/mne/dev/install_mne_c.html

HTH

Alex



> it does other things properly before the error, such as creating the files
> as I said:
> <subj>_brain_surface
> <subj>_inner_skull_surface
> <subj>_outer_skull_surface
> <subj>_inner_skin_surface
>
> Then after some time processing, it raises the error...
>
> ________________________________
>
> De: "Alexandre Gramfort" <alexandre.gramfort at telecom-paristech.fr>
> Para: "Discussion and support forum for the users of MNE Software"
> <mne_analysis at nmr.mgh.harvard.edu>
> Enviadas: Quarta-feira, 4 de Maio de 2016 11:41:35
>
> Assunto: Re: [Mne_analysis] Creating bem meshes with mne_watershed_bem -
> mne_convert_surface not found
>
> ok
>
> now reading in details...
>
> I see:
>
> Command not found: mne_convert_surface
>
> are you sure that you have setup mne in the terminal before running python?
>
> A
>
> On Wed, May 4, 2016 at 3:54 PM,  <milton_avila at usp.br> wrote:
>> Hi Alex!
>> Thanks for the reply.
>>
>> No success. I got the same error.
>> It is happening with the only subject I have.
>> Milton
>> ________________________________
>>
>> De: "Alexandre Gramfort" <alexandre.gramfort at telecom-paristech.fr>
>> Para: "Discussion and support forum for the users of MNE Software"
>> <mne_analysis at nmr.mgh.harvard.edu>
>> Enviadas: Quarta-feira, 4 de Maio de 2016 8:52:07
>> Assunto: Re: [Mne_analysis] Creating bem meshes with mne_watershed_bem -
>> mne_convert_surface not found
>>
>>
>> hi Milton,
>>
>> do you have the problem with all your subjects?
>>
>> if so can you try with the latest version of mne-python code?
>>
>> I recently had to fix this code that was not creating properly the sym
>> links.
>>
>> Alex
>>
>>
>> On Tue, May 3, 2016 at 11:11 PM,  <milton_avila at usp.br> wrote:
>>> Dear MNE users,
>>>
>>> I am trying to create BEM meshes using
>>> mne_watershed_bem.
>>>
>>> I raises the following error:
>>>
>>> Running subprocess: mne_convert_surface --surf S07_brain_surface --mghmri
>>> /media/milton/Dados/MRI/S07/mri/T1.mgz --surfout S07_brain_surface
>>> --replacegeom
>>> Command not found: mne_convert_surface
>>> Traceback (most recent call last):
>>>   File "pre_process.py", line 257, in <module>
>>>     mne.bem.make_watershed_bem(subj, subjects_dir=mri_path,
>>> overwrite=True)
>>>   File "<string>", line 2, in make_watershed_bem
>>>   File "/home/milton/anaconda2/lib/python2.7/site-packages/mne/utils.py",
>>> line 551, in verbose
>>>     return function(*args, **kwargs)
>>>   File "/home/milton/anaconda2/lib/python2.7/site-packages/mne/bem.py",
>>> line
>>> 1015, in make_watershed_bem
>>>     run_subprocess(cmd, env=env, stdout=sys.stdout, stderr=sys.stderr)
>>>   File "<string>", line 2, in run_subprocess
>>>   File "/home/milton/anaconda2/lib/python2.7/site-packages/mne/utils.py",
>>> line 551, in verbose
>>>     return function(*args, **kwargs)
>>>   File "/home/milton/anaconda2/lib/python2.7/site-packages/mne/utils.py",
>>> line 804, in run_subprocess
>>>     p = subprocess.Popen(command, *args, **kwargs)
>>>   File "/home/milton/anaconda2/lib/python2.7/subprocess.py", line 710, in
>>> __init__
>>>     errread, errwrite)
>>>   File "/home/milton/anaconda2/lib/python2.7/subprocess.py", line 1335,
>>> in
>>> _execute_child
>>>     raise child_exception
>>> OSError: [Errno 2] No such file or directory
>>>
>>>
>>> The files created:
>>> <subj>_brain_surface
>>> <subj>_inner_skull_surface
>>> <subj>_outer_skull_surface
>>> <subj>_inner_skin_surface
>>>
>>> The files NOT created:
>>> inner_skull.surf,
>>> outer_skull.surf
>>> outer_skin.surf
>>>
>>> Does anybody know what is going on?
>>> Thanks in advance
>>> Milton
>>>
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> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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