[Mne_analysis] Using standard head

[Vladimir Litvak]

        External Email - Use Caution        

Thank you both. I think I figured it out at least with the GUI. If anyone
has example code for how to scale the head and create individual head from
the average in a script, that could still be helpful (though not critical
at this stage).

Thanks,

Vladimir

On Wed, Sep 19, 2018 at 8:01 AM Maximilien Chaumon <
maximilien.chaumon at gmail.com> wrote:

>         External Email - Use Caution
>
> Hi Vladimir,
> This below should help you:
>
> #!/usr/bin/env python3
> # -*- coding: utf-8 -*-
> """
> create bem model for fsaverage
> This is done only once
> """
>
> import mne
>
> root_dir = '/Your/data/path/'
> subjects_dir = root_dir + 'subjects/'
> mne.set_config('SUBJECTS_DIR',subjects_dir)
> subject = 'fsaverage'
>
> # This defines a source space (a mesh)
> src = mne.setup_source_space(subject=subject,spacing='ico4')
> mne.write_source_spaces(subjects_dir + subject +'/'+
> subject+'-ico4-src.fif',src)
>
> # Create and solve a BEM model takes a few lines
> # following line crashes in my install but I was too lazy to file an
> issue. lines below do the same calling shell scripts
> #mne.bem.make_watershed_bem(subject=subject,overwrite=True)
> from subprocess import call
> code = call(['mne','watershed_bem','-s',subject,'--overwrite'])
> if code:
>     raise ValueError('mne_watershed_bem failed')
>
> # Make BEM
> model = mne.bem.make_bem_model(subject = subject, conductivity=[0.3])
> mne.bem.write_bem_surfaces(subjects_dir+ subject +'/' +
> subject+'-5120-bem.fif', model)
>
> # solve BEM
> bem_sol = mne.bem.make_bem_solution(model)
> mne.bem.write_bem_solution(subjects_dir+ subject +'/' +
> subject+'-5120-bem-sol.fif',bem_sol)
>
> # check that everything completed properly. Compare with online tutorial
> https://www.martinos.org/mne/stable/auto_tutorials/plot_forward.html#sphx-glr-auto-tutorials-plot-forward-py
> mne.viz.plot_bem(subject=subject, subjects_dir=subjects_dir,
>                  brain_surfaces='white', orientation='coronal',
>                  src = subjects_dir + subject +'/'+
> subject+'-ico4-src.fif')
>
> # the following lines will plot your BEM and source model together. (same
> tutorial)
> import numpy as np  # noqa
> from mayavi import mlab  # noqa
> from surfer import Brain  # noqa
>
> brain = Brain('sample', 'lh', 'inflated', subjects_dir=subjects_dir)
> surf = brain.geo['lh']
>
> vertidx = np.where(src[0]['inuse'])[0]
>
> mlab.points3d(surf.x[vertidx], surf.y[vertidx],
>               surf.z[vertidx], color=(1, 1, 0), scale_factor=1.5)
>
>
>
>
> Le mar. 18 sept. 2018 à 20:56, Christian Markus Brodbeck <brodbeck at umd.edu>
> a écrit :
>
>>         External Email - Use Caution
>>
>> Hi Vladimir,
>>
>> The subjects_dir is the directory which will contain your MRI subject
>> folders. It doe snot need to contain any MRIs yet.
>>
>> Christian
>>
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