<div dir="ltr">Hello,<div><br></div><div>I am trying to create an EEG forward model using </div><div><ol><li>anatomy from the sample dataset </li><li>source space from <span style="color:rgb(0,128,128);font-weight:bold;font-family:"Courier New";font-size:9pt">sample_audvis-meg-oct-6-meg-inv.fif</span><br></li><li>standard 1005 montage</li></ol></div><div>When I check the consistency of the coordinate systems with <span style="color:rgb(0,0,0);font-family:"Courier New";font-size:9pt">plot_alignment, </span>I see that the electrode locations are off. </div><div><br></div><div>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?</div><div><br></div><div>Any help will be greatly appreciated.</div><div><br></div><div>Sincerely, Laura Novelinkova</div><div><br></div><div>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 <span style="color:rgb(0,0,0);font-family:"Courier New";font-size:12px">plot_alignment</span>:</div><div><pre style="color:rgb(0,0,0);font-family:"Courier New";font-size:9pt"><span style="color:rgb(0,0,128);font-weight:bold">from </span>mayavi <span style="color:rgb(0,0,128);font-weight:bold">import </span>mlab <span style="color:rgb(128,128,128);font-style:italic"># without this the windows show nothing and hang python<br></span><span style="color:rgb(0,0,128);font-weight:bold">import </span>mne<br><span style="color:rgb(0,0,128);font-weight:bold">from </span>mne.datasets <span style="color:rgb(0,0,128);font-weight:bold">import </span>sample<br><span style="color:rgb(0,0,128);font-weight:bold">import </span>os<br><br>%gui qt<br><br>subject = <span style="color:rgb(0,128,128);font-weight:bold">'sample'<br></span>data_path = sample.data_path()<br>inverse_operator_file_path = os.path.join(data_path, <span style="color:rgb(0,128,128);font-weight:bold">'MEG'</span>, <span style="color:rgb(0,128,128);font-weight:bold">'sample'</span>, <span style="color:rgb(0,128,128);font-weight:bold">'sample_audvis-meg-oct-6-meg-inv.fif'</span>)<br>subjects_dir = os.path.join(data_path, <span style="color:rgb(0,128,128);font-weight:bold">'subjects'</span>)<br><br>montage_1005 = mne.channels.read_montage(<span style="color:rgb(102,0,153)">kind</span>=<span style="color:rgb(0,128,128);font-weight:bold">'standard_1005'</span>)<br>fake_info = mne.create_info(<span style="color:rgb(102,0,153)">ch_names</span>=montage_1005.ch_names, <span style="color:rgb(102,0,153)">sfreq</span>=<span style="color:rgb(0,0,255)">1000</span>, <span style="color:rgb(102,0,153)">ch_types</span>=<span style="color:rgb(0,128,128);font-weight:bold">'eeg'</span>, <span style="color:rgb(102,0,153)">montage</span>=montage_1005)<br>trans = os.path.join(data_path, <span style="color:rgb(0,128,128);font-weight:bold">'MEG'</span>, <span style="color:rgb(0,128,128);font-weight:bold">'sample'</span>, <span style="color:rgb(0,128,128);font-weight:bold">'sample_audvis_raw-trans.fif'</span>)<br>source_space = mne.read_source_spaces(inverse_operator_file_path)<br><br><br>mne.viz.plot_alignment(<span style="color:rgb(102,0,153)">info</span>=fake_info, <span style="color:rgb(102,0,153)">trans</span>=trans, <span style="color:rgb(102,0,153)">subject</span>=subject, <span style="color:rgb(102,0,153)">dig</span>=<span style="color:rgb(0,0,128);font-weight:bold">True</span>,<br> <span style="color:rgb(102,0,153)">meg</span>=<span style="color:rgb(0,0,128);font-weight:bold">False</span>, <span style="color:rgb(102,0,153)">src</span>=source_space, <span style="color:rgb(102,0,153)">subjects_dir</span>=subjects_dir)</pre><pre style="color:rgb(0,0,0);font-family:"Courier New";font-size:9pt"><br></pre><pre style="color:rgb(0,0,0);font-family:"Courier New";font-size:9pt"><img src="cid:ii_15ff8373de6ee475" alt="Inline image 1" width="454" height="421"><br></pre></div></div><div id="DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2"><br>
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