<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 dir="ltr">could you show us how you created the `epochs` variable, and anything you did to it before this failing line? I'm not sure, but it looks like maybe you've got an earlier step in which you needed to include an `epochs.copy()` before doing a pick... many (all?) of the picking methods operate in-place, so if you do first do something like epochs.pick_types(meg=False, eeg=True) then subsequent calls to epochs.pick_types(meg='mag') will fail because after the EEG picking, `epochs` now only contains EEG channels.<br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Nov 6, 2019 at 3:50 PM Megan Schendel <<a href="mailto:mschendel@mrn.org">mschendel@mrn.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p><div dir="ltr">Hi all,<br>Now I'm using mne version 0.19, but I'm still getting pick errors using .pick_types(meg='mag') and (meg='grad'). <div>See below for commands and errors. Any help would be appreciated!</div><div>Thanks,<br>Megan</div><div><br></div><div>In [26]: mne.__version__<br>Out[26]: '0.19.1'<br></div><div><br></div><div>In [27]: mag_epochs = epochs.pick_types(meg='mag')<br> ...:<br>---------------------------------------------------------------------------<br>IndexError Traceback (most recent call last)<br><ipython-input-27-b02891c6983c> in <module><br>----> 1 mag_epochs = epochs.pick_types(meg='mag')<br><br></export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/externals/decorator.py:decorator-gen-31> in pick_types(self, meg, eeg, stim, eog, ecg, emg, ref_meg, misc, resp, chpi, exci, ias, syst, seeg, dipole, gof, bio, ecog, fnirs, include, exclude, selection, verbose)<br><br>/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/utils/_logging.py in wrapper(*args, **kwargs)<br> 88 with use_log_level(verbose_level):<br> 89 return function(*args, **kwargs)<br>---> 90 return function(*args, **kwargs)<br> 91 return FunctionMaker.create(<br> 92 function, 'return decfunc(%(signature)s)',<br><br>/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/channels/channels.py in pick_types(self, meg, eeg, stim, eog, ecg, emg, ref_meg, misc, resp, chpi, exci, ias, syst, seeg, dipole, gof, bio, ecog, fnirs, include, exclude, selection, verbose)<br> 673 ecog=ecog, fnirs=fnirs, include=include, exclude=exclude,<br> 674 selection=selection)<br>--> 675 return self._pick_drop_channels(idx)<br> 676<br> 677 def pick_channels(self, ch_names):<br><br>/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/channels/channels.py in _pick_drop_channels(self, idx)<br> 813<br> 814 if getattr(self, 'picks', None) is not None:<br>--> 815 self.picks = self.picks[idx]<br> 816<br> 817 if hasattr(self, '_cals'):<br><br>IndexError: index 0 is out of bounds for axis 0 with size 0</div><div><br></div><div><br></div><div>In [28]: grad_epochs = epochs.pick_types(meg='grad')<br>---------------------------------------------------------------------------<br>ValueError Traceback (most recent call last)<br><ipython-input-28-ed060676757b> in <module><br>----> 1 grad_epochs = epochs.pick_types(meg='grad')<br><br></export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/externals/decorator.py:decorator-gen-31> in pick_types(self, meg, eeg, stim, eog, ecg, emg, ref_meg, misc, resp, chpi, exci, ias, syst, seeg, dipole, gof, bio, ecog, fnirs, include, exclude, selection, verbose)<br><br>/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/utils/_logging.py in wrapper(*args, **kwargs)<br> 88 with use_log_level(verbose_level):<br> 89 return function(*args, **kwargs)<br>---> 90 return function(*args, **kwargs)<br> 91 return FunctionMaker.create(<br> 92 function, 'return decfunc(%(signature)s)',<br><br>/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/channels/channels.py in pick_types(self, meg, eeg, stim, eog, ecg, emg, ref_meg, misc, resp, chpi, exci, ias, syst, seeg, dipole, gof, bio, ecog, fnirs, include, exclude, selection, verbose)<br> 673 ecog=ecog, fnirs=fnirs, include=include, exclude=exclude,<br> 674 selection=selection)<br>--> 675 return self._pick_drop_channels(idx)<br> 676<br> 677 def pick_channels(self, ch_names):<br><br>/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/channels/channels.py in _pick_drop_channels(self, idx)<br> 818 self._cals = self._cals[idx]<br> 819<br>--> 820 pick_info(<a href="http://self.info" target="_blank">self.info</a>, idx, copy=False)<br> 821<br> 822 if getattr(self, '_projector', None) is not None:<br><br></export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/externals/decorator.py:decorator-gen-8> in pick_info(info, sel, copy, verbose)<br><br>/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/utils/_logging.py in wrapper(*args, **kwargs)<br> 88 with use_log_level(verbose_level):<br> 89 return function(*args, **kwargs)<br>---> 90 return function(*args, **kwargs)<br> 91 return FunctionMaker.create(<br> 92 function, 'return decfunc(%(signature)s)',<br><br>/export/research/analysis/human/jstephen/shared/programs/python/anaconda3/envs/mne19/lib/python3.7/site-packages/mne/io/pick.py in pick_info(info, sel, copy, verbose)<br> 447 return info<br> 448 elif len(sel) == 0:<br>--> 449 raise ValueError('No channels match the selection.')<br> 450 n_unique = len(np.unique(np.arange(len(info['ch_names']))[sel]))<br> 451 if n_unique != len(sel):<br><br>ValueError: No channels match the selection.</div><div><br></div><div><br></div><div><br><div><div dir="ltr"><div dir="ltr"><div>MEG Technician<br>The Mind Research Network<br>1101 Yale Blvd. NE<br>Albuquerque, New Mexico 87106<br><br></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Nov 6, 2019 at 4:23 PM Megan Schendel <<a href="mailto:mschendel@mrn.org" target="_blank">mschendel@mrn.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Thanks, Dan! That worked and will keep me moving!<div>Megan<br><div><div><div dir="ltr"><div dir="ltr"><div>MEG Technician<br>The Mind Research Network<br>1101 Yale Blvd. NE<br>Albuquerque, New Mexico 87106<br><br></div></div></div></div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Nov 6, 2019 at 3:24 PM Dan McCloy <<a href="mailto:dan.mccloy@gmail.com" target="_blank">dan.mccloy@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p><div dir="ltr"><div>I don't know why --only-binary is failing there, but something you could try to get going quickly is to clone one of the existing conda environments, activate the cloned environment, and then do `pip install --upgrade mne` in the new cloned env.</div><div><div dir="ltr"><div dir="ltr">-- dan<br><br>Daniel McCloy<br><a href="http://dan.mccloy.info/" target="_blank">http://dan.mccloy.info/</a><br>Research Scientist<br>Institute for Learning and Brain Sciences<br>University of Washington<br><br></div>
</div>
</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Nov 6, 2019 at 2:10 PM Megan Schendel <<a href="mailto:mschendel@mrn.org" target="_blank">mschendel@mrn.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p><div dir="ltr">Hello again,<br>I'm having trouble trying to update my version of mne.<div>I'm following instructions from
<a href="https://mne.tools/stable/install/mne_python.html" target="_blank">https://mne.tools/stable/install/mne_python.html</a> and I'm trying to use a new anaconda environment so I don't disturb other users who have working scripts with older versions. I didn't get an error with the curl command, but when I try </div><div>conda env create --name mne19 --file environment.yml</div><div>I get </div><div>Using Anaconda Cloud api site <a href="https://api.anaconda.org" target="_blank">https://api.anaconda.org</a><br>Fetching package metadata ...........<br>Solving package specifications: .<br>glib-2.63.1-h5 100% |###########################################################################################| Time: 0:00:00 7.00 MB/s<br>pillow-6.2.1-p 100% |###########################################################################################| Time: 0:00:00 6.81 MB/s<br>jupyter_core-4 100% |###########################################################################################| Time: 0:00:00 9.71 MB/s<br>nbconvert-5.6. 100% |###########################################################################################| Time: 0:00:00 9.09 MB/s<br>ERROR: Invalid requirement: 'dipy --only-binary dipy'<br><br>CondaValueError: pip returned an error.<br><div><div dir="ltr"><div dir="ltr"><div><br></div><div>I know you don't support anaconda, but any insights you could give to this error would be helpful! Or another way to just update the mne install and not the whole anaconda one.</div><div><br></div><div>Thanks,</div><div>Megan</div><div><br></div><div>MEG Technician<br>The Mind Research Network<br>1101 Yale Blvd. NE<br>Albuquerque, New Mexico 87106<br><br></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Nov 1, 2019 at 5:03 PM Megan Schendel <<a href="mailto:mschendel@mrn.org" target="_blank">mschendel@mrn.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Thank you for your help!<div>Megan<br clear="all"><div><div dir="ltr"><div dir="ltr"><div>MEG Technician<br>The Mind Research Network<br>1101 Yale Blvd. NE<br>Albuquerque, New Mexico 87106<br><br></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Oct 30, 2019 at 3:47 AM Alexandre Gramfort <<a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p><div dir="ltr"><div dir="ltr">hi Megan<div><br></div><div>your version of MNE python is too old to pick with a string.</div><div><br></div><div>you need to update or use the old documentation:</div><div><br></div><div><a href="https://mne.tools/0.15/index.html" target="_blank">https://mne.tools/0.15/index.html</a><br></div><div><br></div><div>we are now at version 0.19.1</div><div><br></div><div>Alex</div><div><br></div></div><div class="gmail_quote"></div></div>
_______________________________________________<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" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>
</blockquote></div>
_______________________________________________<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" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>
_______________________________________________<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" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>
</blockquote></div>
_______________________________________________<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" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>