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

[milton_avila at usp.br]

H i Alex! 
Thanks for the reply. 

No success. I got the same error. 
It is happening with the only subject I have. 
Milton 
----- Mensagem original -----

> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160504/f732fc1f/attachment-0001.html