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--></style></head><body lang=EN-US link=blue vlink="#954F72"><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><div class=WordSection1><p class=MsoNormal>When I input `print(raw.ch_names)` before I would get the right channels regardless of capitalization, oddly enough. Although further on in the script it now makes sense that when I would try to do averaging it was telling me that it did not recognize ‘FP1’ as a channel. So, thank you very much Eric, for pointing this difference out. After migrating the code to the suggested commands the montage went from this:</p><p class=MsoNormal align=center style='text-align:center'><img width=328 height=282 style='width:3.4166in;height:2.9375in' id="Picture_x0020_3" src="cid:image002.png@01D5BCFB.51B50A50"></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>To this:<o:p></o:p></p><p class=MsoNormal align=center style='text-align:center'><img width=316 height=282 style='width:3.2916in;height:2.9375in' id="Picture_x0020_4" src="cid:image006.png@01D5BCFB.51B50A50"><o:p></o:p></p><p class=MsoNormal align=center style='text-align:center'><o:p> </o:p></p><p class=MsoNormal>The channel count is accurate now, and the raw.plot output looks exactly as it did before. As for the specifics, when I print(raw.info[‘chs’]) to troubleshoot location it is still off but only by thousandths for the y-axis and hundredths in the y and z axes. Is this a by-product of the aforementioned “shrinking” mentioned before?<o:p></o:p></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:larson.eric.d@gmail.com">Eric Larson</a><br><b>Sent: </b>Friday, December 27, 2019 7:38 PM<br><b>Subject: </b>Re: [Mne_analysis] Conforming to Montage Deprecations</p></div><p class=MsoNormal><o:p> </o:p></p><p><b><span style='color:white;background:red'> External Email - Use Caution </span></b></p><div><p class=MsoNormal>It looks like our standard_1020 names follow a different capitalization pattern:</p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><a href="https://github.com/mne-tools/mne-python/blob/master/mne/channels/data/montages/standard_1020.elc#L107">https://github.com/mne-tools/mne-python/blob/master/mne/channels/data/montages/standard_1020.elc#L107</a></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>So if you do something like:</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>raw.rename_channels(lambda x: x.lower().capitalize())</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Or go the direct dictionary route:</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>raw.rename_channels(dict(FP1='Fp1', OZ='Oz', FZ='Fz', FP2='Fp2', PZ='Pz', CZ='Cz', FPZ='Fpz'))</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Some variant like this should allow not having the warning without needing to pass `raise_if_subset=False`. And if you have channels that are actually not EEG, make sure to do <a href="https://mne.tools/dev/generated/mne.io.Raw.html#mne.io.Raw.set_channel_types">raw.set_channel_types</a> to set them to the correct channel types.</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>As for the channel count mismatch, what extra channels are in raw.ch_names that you don't expect to be there? Does raw.plot() look reasonable?</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Eric</p></div><div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Fri, Dec 27, 2019 at 12:58 AM Bianca Islas <<a href="mailto:biancaisla1@gmail.com">biancaisla1@gmail.com</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><p><b><span style='color:white;background:red'> External Email - Use Caution </span></b></p><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>When I implement the changes this way, I get a ValueError that reads: </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>“DigMontage is a only a subset of info. There are 7 channel positions not present it the DigMontage. The required channels are: {'FP1', 'OZ', 'FZ', 'FP2', 'PZ', 'CZ', 'FPZ'}. You can use `raise_if_subset=False` in `set_montage` to avoid this ValueError and get a DeprecationWarning instead.”</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>If I do as suggested above I do not get an error I get an output of what which channels will be ignored and a warning that reads: </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>“Reading 0 ... 2552079 = 0.000 ... 1276.040 secs...</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><ipython-input-12-e47b0d549095>:8: RuntimeWarning: Could not parse meas date from the header. Setting to None.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> data_format='int32', date_format='mm/dd/yy', preload=True, verbose='debug')</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>DigMontage is a superset of info. 78 in DigMontage will be ignored. The ignored channels are: {'T5', 'Oz', 'C5', 'PO9', 'AF1', 'PO3', 'AF4', 'F1', 'FC4', 'CP3', 'AF6', 'FC6', 'Fz', 'Cz', 'CP5', 'TP7', 'FC3', 'AF8', 'T10', 'P10', 'FT7', 'P6', 'T3', 'TP10', 'PO1', 'AF5', 'P5', 'Iz', 'FC5', 'TP9', 'POz', 'FC2', 'PO8', 'AF3', 'AF10', 'CP2', 'T9', 'PO4', 'PO2', 'FT10', 'P2', 'T6', 'AF7', 'AF9', 'C6', 'A2', 'PO5', 'PO6', 'F6', 'A1', 'P1', 'F10', 'Fp2', 'C2', 'FT8', 'F5', 'AF2', 'P9', 'FCz', 'O9', 'CP4', 'Fp1', 'PO7', 'PO10', 'C1', 'F9', 'CP1', 'O10', 'FT9', 'CP6', 'TP8', 'F2', 'T4', 'CPz', 'Pz', 'AFz', 'Fpz', 'FC1'}</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><ipython-input-12-e47b0d549095>:13: RuntimeWarning: DigMontage is a only a subset of info. Did not set 7 channel positions:</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>FP1, OZ, FZ, FP2, PZ, CZ, FPZ</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> raw.set_montage(montage, raise_if_subset=False)</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Out[12]:</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><RawCNT | st003_PAMR_s1079_20080319.cnt, n_channels x n_times : 38 x 2552080 (1276.0 sec), ~740.0 MB, data loaded>”</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>This is very problematic as I am only supposed to have 23 EEG, 5 EMG, 2 EOG, 1ECG, 2 MISC (skin conductance), and 1 Stim channel.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><ul type=disc><li class=gmail-m1047497547772259800msolistparagraph style='mso-list:l0 level1 lfo1'>Bianca</li></ul><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b>From: </b><a href="mailto:alexandre.gramfort@inria.fr" target="_blank">Alexandre Gramfort</a><br><b>Sent: </b>Thursday, December 26, 2019 11:35 PM<br><b>To: </b><a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">Discussion and support forum for the users of MNE Software</a><br><b>Subject: </b>Re: [Mne_analysis] Conforming to Montage Deprecations</p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> External Email - Use Caution </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>hi Bianca,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>are you doing:</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>raw = mne.io.read_raw_cnt(fname)</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>montage = mne.channels.make_standard_montage(kind=’standard_1020)</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>raw.set_montage(montage)</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>?</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>this should set the chs and the dig.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>the reason we have changed this is that we want to make sure that the channel</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>locations are can considered to be in head coordinate system so you can relate</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>them to fsaverage for example. Is the shrinking problematic for you?</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Alex</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>On Fri, Dec 27, 2019 at 4:43 AM Bianca Islas <<a href="mailto:biancaisla1@gmail.com" target="_blank">biancaisla1@gmail.com</a>> wrote:</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> External Email - Use Caution</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> Happy Holidays MNE Team,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> I am trying to conform to the new deprecation that has occurred in developer version 0.19 concerning the montage. My input file is a Neuroscan (.cnt) file extension type and thus my script previously read `mne.io.read_raw_cnt(fname, montage=’standard_1020’, etc …)`. However, I have migrated this to a separate command `mne.channels.make_standard_montage(kind=’standard_1020)`. When doing this it skews my X,Y,Z locations. For example, when I pass `print(<a href="http://raw.info" target="_blank">raw.info</a>[‘chs’])` my FP1 EEG electrode location is skewed from</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> `’loc’: array([-0.0294367, 0.0839171, -0.00699, 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ])`</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> to</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> `’loc’: array([-0.20257819, 0.21764863, 0.95477283, nan, nan,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> nan, nan, nan, nan, nan,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> nan, nan]).</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> Furthermore, when I input `print(<a href="http://raw.info" target="_blank">raw.info</a>)` the previous code output under `dig : list | 26 items (3 cardinal, 23 EEG)` while the latter code displays NoneType in the `dig`. While this seems like it would be a straight-forward change, it is definitely not as easy in practice. Is there any reason that it is not reading my montage as a standard_1020 anymore?</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> Thank you for any assistance provided,</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> Bianca Islas</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> _______________________________________________</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> Mne_analysis mailing list</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>_______________________________________________</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Mne_analysis mailing list</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div></div></blockquote></div><p class=MsoNormal style='margin-left:4.8pt'>_______________________________________________<br>Mne_analysis mailing list<br><a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br><a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>