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

[Alexandre Gramfort]

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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