[Mne_analysis] Standard montages and coordinate systems

Laura Novelinkova l.novelinkova at gmail.com
Sun Nov 26 07:05:11 EST 2017
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I am trying to create an EEG forward model using

   1. anatomy from the sample dataset
   2. source space from sample_audvis-meg-oct-6-meg-inv.fif
   3. standard 1005 montage

When I check the consistency of the coordinate systems with plot_alignment, I
see that the electrode locations are off.

I think that I need to add transformation information to the info I make
based off the standard montage. Am I right? If yes, could you please advise
me what transformation should I use? And if no, what should I do instead?

Any help will be greatly appreciated.

Sincerely, Laura Novelinkova

Additional info: I am on Windows 7, Python version is 2.7, mne version is
15, I run the code in iPython console. Below is my current code and the
output of plot_alignment:

from mayavi import mlab  # without this the windows show nothing and hang python
import mne
from mne.datasets import sample
import os

%gui qt

subject = 'sample'
data_path = sample.data_path()
inverse_operator_file_path = os.path.join(data_path, 'MEG', 'sample',
subjects_dir = os.path.join(data_path, 'subjects')

montage_1005 = mne.channels.read_montage(kind='standard_1005')
fake_info = mne.create_info(ch_names=montage_1005.ch_names,
sfreq=1000, ch_types='eeg', montage=montage_1005)
trans = os.path.join(data_path, 'MEG', 'sample', 'sample_audvis_raw-trans.fif')
source_space = mne.read_source_spaces(inverse_operator_file_path)

mne.viz.plot_alignment(info=fake_info, trans=trans, subject=subject, dig=True,
                       meg=False, src=source_space, subjects_dir=subjects_dir)

[image: Inline image 1]

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