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
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
> 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
> Mne_analysis Info Page
>
>
> 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
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> you in
> error
> but does not contain patient information, please contact the sender
> and
> properly
> dispose of the e-mail.
>
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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
> 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
>
>
>> 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
>> Mne_analysis Info Page
>>
>>
>> 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
>> MyComplianceReport.com: Compliance and Ethics Reporting . 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
> Mne_analysis Info Page
>
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> Mne_analysis Info Page
>
>
> 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
> MyComplianceReport.com: Compliance and Ethics Reporting . 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 Mne_analysis Info Page