Version 0.23.0 (2021-04-27)

Enhancements

• Add support for exporting to EEGLAB’s set format with eeglabio with new methods mne.io.Raw.export() and mne.Epochs.export(). (#9192 by new contributor Jack Zhang)

• mne.viz.plot_evoked_topo() now uses a Minimum/Maximum of peaks for each channel type to calculate ylim when input param is None (#9285 by new contributor Ram Pari)

• Add exclude parameter to mne.viz.plot_evoked_topo() (#9278 by new contributor Ram Pari)

• Add mne.time_frequency.EpochsTFR.to_data_frame() and mne.time_frequency.AverageTFR.to_data_frame() methods (#9124 by new contributor Felix Klotzsche)

• Add selection and drop_log to mne.time_frequency.EpochsTFR (#9124 by new contributor Felix Klotzsche)

• Add CSV, TSV, and XYZ support to mne.channels.read_custom_montage() (#9203 by new contributor Jack Zhang)

• Add HTML representation for Epochs in Jupyter Notebooks (#9174 by new contributor Valerii Chirkov)

• Speed up mne.viz.plot_ica_properties() by refactoring (#9174 by new contributor Valerii Chirkov)

• Add apply_function method to epochs and evoked objects (#9088 by new contributor Erica Peterson and Victoria Peterson)

• New tutorial for function mne.make_fixed_length_epochs() (#9156 by new contributor Erica Peterson)

• Add different colors for each volume source space in mne.viz.plot_alignment() (#9043 by new contributor Valerii Chirkov)

• Add overlap parameter to mne.make_fixed_length_epochs() to allow creating overlapping fixed length epochs (#9096 by new contributor Silvia Cotroneo)

• Add mne.Dipole.to_mni() for more convenient dipole.pos to MNI conversion (#9043 by new contributor Valerii Chirkov)

• Update citations in maxwell.py (#9043 by new contributor Valerii Chirkov)

• New Tutorial for analyzing frequency-tagging data (#8867 by new contributor Dominik Welke and Evgenii Kalenkovich)

• Add dbs as new channel type for deep brain stimulation (DBS) recordings (#8739 by new contributor Richard Koehler)

• Add some preprocessing functions to the EEGLAB migration guide (#9169 by new contributor Apoorva Karekal)

• Add mne.chpi.extract_chpi_locs_kit() to read cHPI coil locations from KIT/Yokogawa data (#8813 by new contributor Matt Sanderson, Robert Seymour, and Eric Larson)

• Add match_alias parameter to mne.io.Raw.set_montage() and related functions to match unrecognized channel location names to known aliases (#8799 by new contributor Zhi Zhang)

• Update the notebook 3d backend to use ipyvtk_simple for a better integration within Jupyter (#8503 by Guillaume Favelier)

• Remove the 15-character limitation for channel names when writing to FIF format. If you need the old 15-character names, you can use something like raw.rename_channels({n: n[:13] for n in raw.ch_names}, allow_duplicates=True), by Eric Larson (#8346)

• Add channel-specific annotation support to mne.Annotations via ch_names parameter (#8896 by Eric Larson)

• Add toggle-all button to mne.Report HTML and width argument to mne.Report.add_bem_to_section (#8723 by Eric Larson)

• Add infant template MRI dataset downloader mne.datasets.fetch_infant_template() (#8738 by Eric Larson and Christian O’Reilly)

• Add digitizer information to mne.io.read_raw_egi() (#8789 by Christian Brodbeck)

• Add support for reading some incomplete raw FIF files in mne.io.read_raw_fif() (#9268 by Eric Larson)

• Allow reading digitization from files other than *.fif in the coregistration GUI (#8790 by Christian Brodbeck)

• Speed up mne.inverse_sparse.tf_mixed_norm() using STFT/ISTFT linearity (#8697 by Eric Larson)

• Reduce memory consumption of mne.io.Raw and speed up epoching when thousands of events are present for mne.Epochs (#8801 by Eric Larson)

• Speed up import mne by reducing function creation overhead (#8829 by Eric Larson)

• mne.Report.parse_folder now processes supported non-FIFF files by default, too (#8744 by Richard Höchenberger)

• mne.Report has gained the new methods add_custom_js and add_custom_css for adding user-defined JavaScript and styles (#8762, #9037 by Richard Höchenberger)

• Add option to control appearance of opaque inside surface of the head to mne coreg (#8793 by Eric Larson)

• Add option to disable projection using --projoff in mne browse_raw (#9262 by Eric Larson)

• Add keypress to toggle projection using shift+j in mne.io.Raw.plot() and mne browse_raw (#9262 by Eric Larson)

• Add support for non-FIF files in mne browse_raw using mne.io.read_raw() (#8806 by Eric Larson)

• Add mne.io.read_raw_nedf() for reading StarStim / enobio NEDF files (#8734 by Tristan Stenner)

• Add raw.describe() to display (or return) descriptive statistics for each channel (#8760 by Clemens Brunner)

• Add annotations.to_data_frame() to return annotations as a pandas dataframe (#8783 by Robert Luke)

• Add mne.preprocessing.compute_maxwell_basis() to compute the SSS basis function (#8822 by Eric Larson)

• Add the silhouette parameter to mne.viz.Brain to display sharp edges and improve perception (#8771 by Guillaume Favelier)

• Add warning to mne.cov.compute_whitener() when an explicit rank parameter leads to a large increase in condition number (#8805 by Eric Larson)

• Add parameter align=True to mne.viz.Brain.show_view to make views relative to the closest canonical (MNI) axes rather than the native MRI surface RAS coordinates (#8794 by Eric Larson)

• Add auto_close to mne.Report.add_figs_to_section and mne.Report.add_slider_to_section to manage closing figures (#8730 by Guillaume Favelier)

• Add mne.write_head_bem() to support writing head surface files (#8841 by Yu-Han Luo)

• The signal of resp (respiratory) channels is now assumed to be in the unit Volt (#8858 by Richard Höchenberger)

• Static type checkers like Pylance (comes with VS Code) now display the parameters of many more functions correctly, largely improving overall usability for VS Code users (#8862 by Richard Höchenberger)

• Support new EEGLAB file format (#8874 by Clemens Brunner)

• Reading and writing FIFF files whose filenames end with _meg.fif.gz, _eeg.fif(.gz), and _ieeg.fif(.gz) doesn’t emit a warning anymore; this improves interobaility with BIDS-formatted datasets (#8868 by Richard Höchenberger)

• On macOS, we now set the environment variable QT_MAC_WANTS_LAYER to "1" if it hasn’t been set explicitly by the user, in order to ensure that SourceEstimate plots work on macOS 11 with older versions of Qt and PyQt (#8959 by Richard Höchenberger)

• mne.time_frequency.EpochsTFR.average() now allows different ways of averaging, such as “median”, or callable functions (#8879 by Adam Li)

• Epochs metadata can now be generated automatically from events using mne.epochs.make_metadata (#8834 by Richard Höchenberger)

• Interactions with sliders in mne.Report will now continuously update the linked content (it was updated only on mouse button release before) (#9023 by Richard Höchenberger)

• mne.viz.plot_drop_log and mne.Epochs.plot_drop_log() now omit displaying the subject name in the title if subject=None is passed (#9015 by Richard Höchenberger)

• Plot ECoG tutorial now uses a real epilepsy seizure dataset and visualizes the seizure onset (#9087 by Eric Larson, Adam Li, Alex Rockhill and Liberty Hamilton)

• Improve documentation of Report-Class (#9113 by Martin Schulz)

• Add mne.channels.DigMontage.add_estimated_fiducials() which will add LPA, RPA and Nasion fiducial points to the DigMontage object in mri coordinate frame (#9118 by Adam Li)

• mne.io.anonymize_info() now anonymizes also sex and hand fields when keep_his is False (#9103, #9175 by new contributor Rotem Falach and Richard Höchenberger)

• Add parameter theme to mne.viz.Brain for optional Dark-Mode (#9149 by Martin Schulz, Guillaume Favelier)

• Add first_samp support for raw simulations with mne.simulation.simulate_raw and mne.simulation.SourceSimulator (#9166 by Steven Bierer)

• Evoked gained a baseline attribute that is automatically assembled based on the baseline of the averaged Epochs (#9210 by Richard Höchenberger)

• Add units parameter to mne.io.Raw.get_data() to return data in the desired unit (#9136 by Johann Benerradi and Stefan Appelhoff)

• Add mne.preprocessing.equalize_bads() to interpolate bad channels in a list of Evoked, Epochs or Raw having different sets of bad channels (#9241 by Alex Gramfort)

• mne.Epochs.equalize_event_counts() can now be called without providing a list of event names, and will equalize the counts of all event types present in the Epochs (#9261 by Richard Höchenberger)

• mne.preprocessing.find_eog_events() and mne.preprocessing.create_eog_epochs() now accept a list of channel names, allowing you to specify multiple EOG channels at once (#9269 by Richard Höchenberger)

• Improve performance of mne.set_bipolar_reference() (#9270 by Martin Schulz)

• Add support for setting montages on fNIRS data, with built in standard montages for Artinis OctaMon and Artinis Brite23 devices (#9141 by Johann Benerradi, Robert Luke and Eric Larson)

• Enable support for reading SNIRF files with 2D optode positions (#9347 Robert Luke)

Bugs

• Fix bug with mne.time_frequency.tfr() where plot misbehaved. Plot now always returns a list of figures instead of a single figure handle (#8013 by new contributor Eduard Ort)

• Fix bug with mne.viz.plot_evoked_topo() where set ylim parameters gets swapped across channel types. (#9207 by new contributor Ram Pari)

• Fix bug with mne.io.read_raw_edf() where µV was not correctly recognized (#9187 by new contributor Sumalyo Datta)

• Fix bug with mne.viz.plot_compare_evokeds() did not check type of combine. (#9151 by new contributor Matteo Anelli)

• Fix bug with mne.viz.plot_evoked_topo() where ylim was only being applied to the first channel in the dataset (#9162 by new contributor Ram Pari )

• Fix bug with mne.Epochs.plot_image() allowing interactive zoom to work properly (#9152 by by new contributor Maggie Clarke and Daniel McCloy)

• Fix bug with mne.Epochs.plot_image() where the x_label was different depending on the evoked parameter (#9115 by new contributor Matteo Anelli)

• Fix bug with restricting mne.io.Raw.save() saving options to .fif and .fif.gz extensions (#9062 by new contributor Valerii Chirkov)

• Fix bug with mne.io.read_raw_kit() where missing marker coils were not handled (#8989 by new contributor Judy D Zhu)

• Fix bug with mne.connectivity.spectral_connectivity where time axis in Epochs data object was dropped. (#8839 by new contributor Anna Padee)

• Fix bug with mne.io.Raw.resample to allow passing stim_picks='misc' (#8844 by new contributor Enrico Varano and Eric Larson)

• Fix bugs with mne.io.read_raw_persyst where multiple Comments with the same name are allowed, and Comments with a “,” character are now allowed (#8311 and #8806 by new contributor Andres Rodriguez and Adam Li)

• Fix zen mode and scalebar toggling for raw.plot() when using the macosx matplotlib backend (#8688 by Daniel McCloy)

• Fix bug with mne.viz.snapshot_brain_montage() where the positions were incorrect (#8983 by Eric Larson)

• Fix bug with mne.preprocessing.maxwell_filter() where the eSSS basis had to exactly match the good channels instead of being a superset (#8675 by Eric Larson)

• Fix bug with mne.Report.add_bem_to_section where n_jobs != 1 would cause n_jobs subsets of MRI images in some orientations to be flipped (#8713 by Eric Larson)

• Fix bug with raw.plot() where annotations didn’t immediately appear when changing window duration (#8689 by Daniel McCloy)

• Fix bug with raw.plot() where scalings='auto' did not compute scalings using the full range of data (#8806 by Eric Larson)

• Fix bug with raw.plot() where setting a lowpass could lead to non-data-channels not plotting (#8954 by Eric Larson)

• Fix bug with mne.io.Raw.load_data() and mne.Epochs.drop_bad() where verbose logging was not handled properly (#8884 by Eric Larson)

• Fix bug with mne.io.read_raw_nicolet() where header type values such as num_sample and duration_in_sec where not parsed properly (#8712 by Alex Gramfort)

• Fix bug with mne.preprocessing.read_ica_eeglab() when reading decompositions using PCA dimensionality reduction (#8780 by Alex Gramfort and Eric Larson)

• Fix bug with mne.minimum_norm.make_inverse_operator() where depth was errantly restricted to be less than or equal to 1. (#8804 by Eric Larson)

• Fix bug with mne.stats.permutation_cluster_1samp_test() and related clustering functions when adjacency=None and out_type='indices' (##8842 by Eric Larson)

• Fix bug with mne.viz.plot_alignment() where plotting a sphere model could ignore the brain argument (#8857 by Eric Larson)

• Fix bug with mne.SourceEstimate.plot() where flatmaps were not positioned properly when using hemi='both' (#9315 by Eric Larson)

• Fix bug with mne.Annotations.save() where files could be overwritten accidentally, it can now be controlled via the overwrite argument (#8896 by Eric Larson)

• Fix bug with replace argument of mne.Report.add_bem_to_section and mne.Report.add_slider_to_section (#8723 by Eric Larson)

• Fix bug with mne.chpi.compute_chpi_locs() where all cHPI coils being off would lead to an empty array of the wrong dimensionality (#8956 by Eric Larson)

• Fix bug with mne.extract_label_time_course() where labels, STCs, and the source space were not checked for compatible subject attributes (#9284 by Eric Larson)

• Fix bug with mne.grow_labels() where overlap=False could run forever or raise an error (#9317 by Eric Larson)

• Fix compatibility bugs with mne_realtime (#8845 by Eric Larson)

• Fix bug with mne.viz.Brain where non-inflated surfaces had an X-offset imposed by default (#8794 by Eric Larson)

• Fix bug with mne coreg where nasion values were not updated when clicking (#8793 by Eric Larson)

• Fix bug with matplotlib-based 3D plotting where Axes3D were not properly initialized in mne.viz.plot_source_estimates() (#8811 by Chris Bailey)

• Allow sEEG channel types in mne.Evoked.plot_joint() (#8736 by Daniel McCloy)

• Fix bug where hidden annotations could be deleted interactively in mne.io.Raw.plot() windows (#8831 by Daniel McCloy)

• Function mne.set_bipolar_reference() was not working when passing Epochs constructed with some picks (#8728 by Alex Gramfort)

• Fix anonymization issue of FIF files after IO round trip (#8731 by Alex Gramfort)

• Fix bug in mne.preprocessing.ICA.plot_sources where right-clicking component names could yield plot_properties windows for the wrong component if picks had been specified (#8996 by Daniel McCloy)

• Fix title not shown in mne.viz.plot_montage() (#8752 by Clemens Brunner)

• mne.io.read_raw_egi now correctly handles pathlib.Path filenames (#8759 by Richard Höchenberger)

• mne.viz.plot_evoked and mne.Evoked.plot now correctly plot global field power (GFP) for EEG data when gfp=True or gfp='only' is passed (used to plot RMS). For MEG data, we continue to plot the RMS, but now label it correctly as such (#8775 by Richard Höchenberger)

• Fix bug with mne make_scalp_surfaces where --overwrite was not functional (#8800 by Yu-Han Luo)

• Fix bug with mne.viz.plot_topomap() when plotting gradiometers with a missing channel in a pair (#8817 by Alex Gramfort)

• epochs.crop() now also adjusts the reject_tmin and reject_tmax attributes if necessary (#8821 by Richard Höchenberger)

• When creating Epochs, we now ensure that reject_tmin and reject_tmax cannot fall outside of the epochs’ time interval anymore (#8821 by Richard Höchenberger)

• read_raw_bti erroneously treated response channels as respiratory channels (#8856 by Richard Höchenberger)

• The RMS trace shown in the time viewer of SourceEstimate plots is now correctly labeled as RMS (was GFP before) (#8965 by Richard Höchenberger)

• Fix bug with mne.SourceEstimate.plot() and related functions where the scalars were not interactively updated properly (#8985 by Eric Larson)

• Fix bug with mne.channels.find_ch_adjacency() returning wrong adjacency for Neuromag122-Data (#8891 by Martin Schulz)

• Fix mne.read_dipole() yielding mne.Dipole objects that could not be indexed (#8963 by Marijn van Vliet)

• Fix bug when setting n_jobs > 1 in mne.Report.parse_folder() (#9109 by Martin Schulz)

• Fix bug with mne.Evoked.plot_image() where an incorrect clim parameter did not raise any error (#9115 by new contributor Matteo Anelli)

• Fix bug with mne.io.Raw.pick where incorrect fnirs types were returned (#9178 by Robert Luke)

• Fix bug when passing both axes and picks to mne.viz.plot_compare_evokeds (#9252 by Daniel McCloy)

• Improved string representation of Epochs containing multiple event types; improved (and more mathematically correct) evoked.comment in the mne.combine_evoked output; and better (and often more concise) legend labels in the figures created via plot_compare_evokeds (#9027 by Richard Höchenberger)

• mne.preprocessing.find_ecg_events() now correctly handles situation where no ECG activity could be detected, and correctly returns an empty array of ECG events (#9236 by Richard Höchenberger)

• Fix bug with picks attribute for Epochs after calling mne.Epochs.add_channels() (#9246 by Alex Gramfort)

• Fix bug where backend='notebook' could not be used in mne.SourceEstimate.plot() (#9305 by Jean-Rémi King)

• mne.preprocessing.compute_proj_eog and mne.preprocessing.compute_proj_ecg now return empty lists if no EOG or ECG events, respectively, could be found. Previously, we’d return None in these situations, which does not match the documented behavior of returning a list of projectors (#9277 by Richard Höchenberger)

API changes

• Introduced new 'auto' settings for ICA.max_iter. The old default max_iter=200 will be removed in MNE-Python 0.24 (#9099 by new contributor Cora Kim)

• mne.viz.plot_sensors_connectivity now allows setting the colorbar label via the cbar_label parameter (#9248 by Daniel McCloy)

• mne.read_selection has been deprecated in favor of mne.read_vectorview_selection. mne.read_selection will be removed in MNE-Python 0.24 (#8870 by Richard Höchenberger)

• mne.beamformer.tf_dics has been deprecated and will be removed in MNE-Python 0.24 (#9122 by Britta Westner)

• Fitting ICA on baseline-corrected Epochs, and / or applying it on baseline-corrected Epochs or Evoked data will now display a warning. Users are advised to only baseline correct their data after cleaning is completed (#9033 by Richard Höchenberger)

• Supplying multiple channel names to mne.preprocessing.find_eog_events or mne.preprocessing.compute_proj_eog as a string of comma-separated channel names has been deprecated; please pass a list of channel names instead. Support for comma-separated strings will be removed in MNE-Python 0.24 (#9269 by Richard Höchenberger)

• The default in mne.beamformer.make_dics() of real_filter=False will change to real_filter=True in 0.24 (#9340 by Britta Westner)

Authors

People who contributed to this release in alphabetical order (people with a + are first time contributors):

• Adam Li

• Alex Rockhill

• Alexandre Gramfort

• Ana Radanovic

• Andres Rodriguez+

• Anna Padee+

• Apoorva Karekal+

• Britta Westner

• Catalina Magalvan

• Christian Brodbeck

• Christian Mista

• Christian O’Reilly

• Christina Zhao

• Christopher J. Bailey

• Clemens Brunner

• Cora Kim+

• Daniel McCloy

• Denis A. Engemann

• Dominik Welke+

• Eduard Ort

• Enrico Varano+

• Eric Larson

• Erica Peterson+

• Evgenii Kalenkovich

• Felix Klotzsche+

• Giorgio Marinato

• Guillaume Favelier

• Jack Zhang+

• Jean-Rémi King

• Johann Benerradi

• Joris Van den Bossche

• Judy D Zhu+

• Liberty Hamilton

• Luke Bloy

• Maggie Clarke+

• Mainak Jas

• Manorama Kadwani

• Marijn van Vliet

• Martin Schulz

• Matt Sanderson+

• Matteo Anelli+

• Nicolas Gensollen

• Ram Pari+

• Richard Höchenberger

• Richard Koehler+

• Robert Luke

• Rotem Falach+

• Sebastien Treguer

• Silvia Cotroneo+

• Stefan Appelhoff

• Steven Bierer

• Sumalyo Datta+

• Timon Merk

• Tristan Stenner

• Valerii Chirkov+

• Victoria Peterson

• Yu-Han Luo

• Zhi Zhang+