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

milton_avila at usp.br milton_avila at usp.br
Wed May 4 12:17:26 EDT 2016
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Yes, 
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... 

----- 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 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
> >>
> >> _______________________________________________
> >> Mne_analysis mailing list
> >> Mne_analysis at nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >>
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