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

[Alexandre Gramfort]

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
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> 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
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it is
> 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
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>