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<body lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"><p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p>
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<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Hi Eric,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Thank you for the reply.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">I do not apply the projectors to the data, the code is:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"> # Load<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US">raw = mne.io.read_raw_fif(fname, preload=True)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US">raw.set_channel_types(mapping={'ECG':'ecg', 'EOG':'eog'})<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US">raw.set_montage('standard_1020')<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US">raw.info['bads'] = list()<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US"># Conversion<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US">raw.apply_function(conversion_uVolt2Volt, picks=['ecg', 'eog', 'eeg'], dtype=None,
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US"> n_jobs=1, channel_wise=True, verbose=None)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US">raw.apply_function(brainvisionMarkersCh2StimCh, picks=['stim'], dtype=None,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US"> n_jobs=1, channel_wise=True, verbose=None)<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US"># Car and filters<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US">raw.set_eeg_reference(ref_channels='average', ch_type='eeg', projection=True)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US">mne.io.Raw.filter(raw, l_freq=1., h_freq=100., picks=['ecg', 'eog', 'eeg'], method='iir',
<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US"> iir_params=dict(order=4, ftype='butter', output='sos'))<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US">raw.notch_filter(np.arange(50, 151, 50), picks=['ecg', 'eog'], filter_length='auto', phase='zero')<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US"># Plot<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span lang="EN-US" style="mso-fareast-language:EN-US">raw.plot(scalings=dict(eeg=20e-6, eog=4e-2, ecg=5e-2, stim=2))<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">In the plot interface, the CAR projector is selected in the bottom right projector panel.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">When in the plot I click on a channel to mark it as bad (changing its color to light grey), the others do not change at all, thus I don’t think the projector is updated on my setup.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Mathieu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black"><mne_analysis-bounces@nmr.mgh.harvard.edu> on behalf of Eric Larson <larson.eric.d@gmail.com><br>
<b>Reply to: </b>Discussion and support forum for the users of MNE Software <Mne_analysis@nmr.mgh.harvard.edu><br>
<b>Date: </b>Tuesday, 15 December 2020 at 18:59<br>
<b>To: </b>Discussion and support forum for the users of MNE Software <Mne_analysis@nmr.mgh.harvard.edu><br>
<b>Subject: </b>Re: [Mne_analysis] Inputting bad channels through raw.plot() while applying a CAR reference. {Disarmed}<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">When applying a CAR (as a projector), MNE removes the already set
<a href="http://secure-web.cisco.com/1Z5R3lf4_Yhc3f-8tcRLDANtB_KwN4pLGbSuFpRLxU1AF4atIofcrktKaEDvZRxIf17jXo8CjVhq_M1Ag-hLXAPQorOED0O3y6sqtUKhUSxYmno8YfvJn7WWLUF_vNNv78K9vXpLNzY0EmEYTYJzvl1qljUaKQ6JzVdZATHuiVjdXfh0iLr52ifZm_FwLBPTfnU6e9v86Fe90V-JNAOCf0epQZs3lRAmJyVKKdy9LZAp21URuxEa7X2mWki9UY6nfH1En5Q7Gi1J9yUn8SrfXLg/http%3A%2F%2Fraw.info" target="_blank">
<b><span style="color:red">MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be</span></b> raw.info</a>[‘bads’] from the average. However, when adding or removing bad channels through the plot interface, I guess the CAR
projector is not updated.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">As long as you don't `raw.apply_proj()`, then in `raw.plot` or `mne browse_raw` the CAR projector should be updated. If it's not, there is a bug -- feel free to open one on GitHub.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Eric<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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