Version 1.0.0 (2022-03-21)

Enhancements

• Add use_orig_time option to mne.Annotations.crop(). (#10396 by new contributor Michiru Kaneda)

• Speed up mne.preprocessing.annotate_muscle_zscore(), mne.preprocessing.annotate_movement(), and mne.preprocessing.annotate_nan() through better annotation creation (#10089 by new contributor Senwen Deng)

• Fix some unused variables in time_frequency_erds.py example (#10076 by new contributor Jan Zerfowski)

• Document BAD_ACQ_SKIP annotation behavior (#10054 by new contributor Etienne de Montalivet)

• Add link to related MNE-ARI package (#10174 by new contributor John Veillette)

• mne.time_frequency.psd_array_multitaper() can now return complex results per-taper when specifying output='complex' (#10307 by Mikołaj Magnuski)

• mne.time_frequency.tfr_array_multitaper() can now return results for output='phase' instead of an error (#10281 by Mikołaj Magnuski)

• Add show local maxima toggling button to mne.gui.locate_ieeg (#9952 by Alex Rockhill)

• Show boundaries in mne.gui.locate_ieeg (#10379 by Eric Larson)

• Add argument cval to mne.transforms.apply_volume_registration() to set interpolation values outside the image domain (#10379 by Eric Larson)

• Improve docstring of mne.Info and add attributes that were not covered (#9922 by Mathieu Scheltienne)

• Add an alternate, manual procedure for aligning a CT to an MR procedure to Locating intracranial electrode contacts (#9978 by Alex Rockhill)

• Improve docstring of export functions mne.export.export_raw(), mne.export.export_epochs(), mne.export.export_evokeds(), mne.export.export_evokeds_mff() and issue a warning when there are unapplied projectors (#9994 by Mathieu Scheltienne)

• Add support for reading haemoglobin fNIRS data to mne.io.read_raw_snirf() (#9929 by Robert Luke)

• Add fill_hole_size keyword argument to mne.viz.Brain.add_volume_labels() to close holes in the mesh (#10024 by Alex Rockhill)

• Changed mne.Epochs and mne.Evoked to have a more concise __repr__ to improve interactive MNE usage in Python Interactive Console, IDEs, and debuggers when many events are handled. (#10042 by Jan Sosulski)

• Improve docstring of events arguments and cross-referencing to events (#10056 by Mathieu Scheltienne)

• Speed up repeated surface-smoothing operation (e.g., in repeated calls to stc.plot()) (#10077 by Eric Larson)

• Add verbose parameter to mne.io.Raw.load_bad_channels() and log information on how bad channels are updated (#10102 by Stefan Appelhoff)

• Add infer_type argument to mne.io.read_raw_edf() and mne.io.read_raw_bdf() to automatically infer channel types from channel labels (#10058 by Clemens Brunner)

• Reduce the time it takes to generate a mne.io.Raw, Epochs, or ICA figure if a scalings parameter is provided (#10109 by Richard Höchenberger and Eric Larson)

• mne.Report.add_raw() gained a new scalings parameter to provide custom data scalings for the butterfly plots (#10109 by Richard Höchenberger)

• The butterfly parameter of mne.Report.add_raw() now also accepts numbers to specify how many segments to plot (#10115 by Richard Höchenberger)

• The psd parameter of mne.Report.add_epochs() now also accepts numbers to specify the signal duration used for PSD calculation (#10119 by Richard Höchenberger)

• Drastically speed up butterfly plot generation in mne.Report.add_raw(). We now don’t plot annotations anymore; however, we feel that the speed improvements justify this change, also considering the annotations were of limited use in the displayed one-second time slices anyway (#10114, #10116 by Richard Höchenberger)

• In mne.Report, limit the width of automatically generated figures to a maximum of 850 pixels (450 pixels for mne.SourceEstimate plots), and the resolution to 100 DPI to reduce file size, memory consumption, and – in some cases like mne.Report.add_stc() – processing time (#10126, #10129, #10135, #10142 by Richard Höchenberger)

• Epochs metadata tables are now included in mne.Report (#10166 by Richard Höchenberger)

• mne.get_head_surf() and mne.dig_mri_distances() gained a new parameter, on_defects, controlling how to handle surfaces with topological defects (#10175 by Richard Höchenberger)

• mne.Report.add_epochs() gained a new parameter, drop_log_ignore, to control which drop reasons to omit when creating the drop log plot (#10182 by Richard Höchenberger)

• mne.Epochs.plot_drop_log() now also includes the absolute number of epochs dropped in the title (#10186 by Richard Höchenberger)

• Add a button to show the maximum intensity projection in mne.gui.locate_ieeg (#10185 by Alex Rockhill)

• Annotations from a Raw object are now preserved by the Epochs constructor and are supported when saving Epochs (#9969 and #10019 by Adam Li)

• Add a checkbox to show and hide the MEG helmet in the coregistration GUI (#10200 by Guillaume Favelier)

• The coregistration GUI (instantiated via mne.gui.coregistration()) gained a new attribute, coreg, to access the mne.coreg.Coregistration instance used by the GUI (#10255 by Richard Höchenberger)

• Add marching cubes display of head if mne.bem.make_scalp_surfaces() has not computed or the recon-all hasn’t finished (#10202 by Alex Rockhill)

• The default interaction style of mne.gui.coregistration() and mne.viz.plot_alignment() has been changed to 'terrain', which keeps one axis fixed and should make interactions with the 3D scene more predictable (#9972, #10206 by Richard Höchenberger)

• mne.gui.coregistration() now uses the proper widget style for push buttons, making for a more native feel of the application (#10220 by Richard Höchenberger and Guillaume Favelier)

• mne.coreg.Coregistration, mne.scale_bem(), and mne.scale_mri() gained a new parameter, on_defects, controlling how to handle topological defects (#10230, #10249 by Richard Höchenberger)

• mne.coreg.Coregistration gained a new attribute, fiducials, allowing for convenient retrieval of the MRI fiducial points (#10243, by Richard Höchenberger)

• Added plotting points to represent contacts on the max intensity projection plot for mne.gui.locate_ieeg (#10212 by Alex Rockhill)

• Add lines in 3D and on the maximum intensity projection when more than two electrode contacts are selected to aid in identifying that contact for mne.gui.locate_ieeg (#10212 by Alex Rockhill)

• Add a block parameter to mne.viz.Brain and the UI of mne.coreg.Coregistration to prevent the windows from closing immediately when running in a non-interactive Python session (#10222 by Guillaume Favelier)

• All methods of mne.Report with a tags parameter now also accept a single tag passed as a string (previously, you needed to pass a tuple of strings, even for a single tag) (#10183, by Richard Höchenberger)

• mne.Report.add_trans() has gained a new parameter, alpha, to control the level of opacity of the rendered head (#10247, by Richard Höchenberger)

• The new convenience function mne.event.match_event_names() allows for straightforward checking if a specific event name or a group of events is present in a collection of event names (#10233 by Richard Höchenberger)

• Epochs.plot() is now supported by the pyqtgraph-backend (#10297 by Martin Schulz)

• The map_surface parameter of mne.viz.Brain.add_foci() now works and allows you to add foci to a rendering of a brain that are positioned at the vertex of the mesh closest to the given coordinates (#10299 by Marijn van Vliet)

• mne.preprocessing.ICA.plot_sources() is now also supported by the qt backend (#10330 by Martin Schulz)

• Added mne.viz.Brain.add_dipole() and mne.viz.Brain.add_forward() to plot dipoles on a brain as well as mne.viz.Brain.remove_dipole() and mne.viz.Brain.remove_forward() (#10373 by Alex Rockhill)

• Made anterior/posterior slice scrolling in mne.gui.locate_ieeg possible for users without page up and page down buttons by allowing angle bracket buttons to be used (#10384 by Alex Rockhill)

• Add support for theme='auto' for automatic dark-mode support in raw.plot() and related functions and methods when using the 'qt' backend (#10417 by Eric Larson)

• Add support for MNE_3D_OPTION_THEME and MNE_BROWSER_THEME to use ['light', 'dark', 'auto'] or a custom theme path in mne.viz.Brain and raw.plot() (and related functions and methods when using the 'qt' backend(), respectively (#10418 by Eric Larson)

• Add support for passing time-frequency data to mne.stats.spatio_temporal_cluster_test() and mne.stats.spatio_temporal_cluster_1samp_test() and added an example to Spatiotemporal permutation F-test on full sensor data (#10384 by Alex Rockhill)

• Add support for reading optical density fNIRS data to mne.io.read_raw_snirf() (#10408 by Robert Luke)

• Added mne.source_space.get_decimated_surfaces() to extract subsurfaces from a SourceSpaces instance or a .fif file (#10421 by Joshua Teves)

Bugs

• Fix bug with mne.io.read_raw_nihon() where latin-1 channels could not be read (#10429 by new contributor Matthias Eberlein)

• Fix bug with mne.io.read_raw_nihon() so that it handles duplicates in channel names (#10431 by new contributor Matthias Eberlein)

• Fix bug in mne.io.read_raw_egi() where the meas_date in a rawMFF object was incorrectly assigned. The function now converts the meas_date to UTC and provides a UTC offset key, i.e. raw.info['utc_offset']. (#10304 by new contributor Scott Huberty)

• Fix datetime conversion for tmin/tmax=None cases in mne.Annotations.crop(). Allow the use of float and None simultaneously for mne.Annotations.crop(). (#10361 by new contributor Michiru Kaneda)

• Add Shift_JIST mu in mne.io.read_raw_edf() (#10356 by new contributor Michiru Kaneda)

• Teach mne.io.read_raw_bti() to use its eog_ch parameter (#10093 by new contributor Adina Wagner)

• Fix use of arguments in numpy.loadtxt() (#10189 by new contributor Federico Zamberlan)

• Fix documentation of options in mne.stc_near_sensors() (#10007 by new contributor Nikolai Chapochnikov)

• mne.time_frequency.tfr_array_multitaper() now returns results per taper when output='complex' (#10281 by Mikołaj Magnuski)

• Fix default of mne.io.Raw.plot() to be use_opengl=None, which will act like False unless MNE_BROWSER_USE_OPENGL=true is set in the user configuration (#9957 by Eric Larson)

• Fix bug with mne.Report where figures were saved with bbox_inches='tight', which led to inconsistent sizes in sliders (#9966 by Eric Larson)

• When opening a saved report and saving it to a different filename again, don’t change Report.fname to avoid a regression when using open_report() as a context manager (#9998 by Marijn van Vliet)

• Fix bug in mne.make_forward_solution() where sensor-sphere geometry check was incorrect (#9968 by Eric Larson)

• Use single char alphanumeric suffix when renaming long channel names (over 15-characters) when writing to FIF format. (#10002 by Luke Bloy)

• Add argument overwrite to mne.export.export_raw(), mne.export.export_epochs(), mne.export.export_evokeds() and mne.export.export_evokeds_mff() (#9975 by Mathieu Scheltienne)

• mne.gui.coregistration() and the mne coreg command didn’t respect the interaction parameter (#9972 by Richard Höchenberger)

• Fix incorrect projection of source space onto white matter surface instead of pial in Working with ECoG data (#9980 by Alex Rockhill)

• Fix channel type support when reading from EEGLAB .set format with mne.io.read_raw_eeglab() and mne.read_epochs_eeglab() (#9990 by Mathieu Scheltienne)

• Fix suboptimal alignment using mne.transforms.compute_volume_registration() (#9991 by Alex Rockhill)

• Only warn if header is missing in BrainVision files instead of raising an error (#10001 by Clemens Brunner)

• Add argument overwrite to mne.preprocessing.ICA.save to check for existing file (#10004 by Mathieu Scheltienne)

• mne.Report now raises an exception if invalid tags were passed (#9970 by Richard Höchenberger)

• Fix bug in mne.get_montage_volume_labels() that set the maximum number of voxels to be included too low causing unwanted capping of the included voxel labels (#10021 by Alex Rockhill)

• Fix annotation cropping and I/O roundtrip when there is no measurement date available (#10040 by Mathieu Scheltienne and Alex Gramfort).

• Fix bug where raw.crop() from the beginning of the instance could break annotations and raw.first_samp (#10358 by Eric Larson)

• sys_info() output now contains the installed version of pooch, too; this output had been accidentally removed previously (#10047 by Richard Höchenberger)

• Fix VTK version extraction in mne.sys_info() (#10399 by Eric Larson)

• Fix automatic channel type detection from channel labels in mne.io.read_raw_edf() and mne.io.read_raw_bdf() (and disable this functionality from mne.io.read_raw_gdf()) (#10058 by Clemens Brunner)

• Fix permutation_cluster_1samp_test() to properly handle 2-dimensional data in combination with TFCE (#10073 by Richard Höchenberger)

• Fix channel grouping error when using “butterfly mode” with mne.io.Raw.plot() (#10087 by Daniel McCloy)

• Fix inconsistent behavior of mne.preprocessing.annotate_* functions by making them all return mne.Annotations objects with the orig_time attribute set to raw.info["meas_time"] (#10067 and #10118 by Stefan Appelhoff, Eric Larson, and Alex Gramfort)

• Fix bug that appears during automatic calculation of the colormap of mne.viz.Brain when data values of fmin and fmax are too close (#10074 by Guillaume Favelier)

• We now display a scrollbar in the tags dropdown of a Report if many tags have been added, granting access to all tags instead of “hiding” them below the bottom of the page (#10082 by Richard Höchenberger)

• Creating mne.Epochs now provides clearer logging (less ambiguous, no duplicates) when the preload and/or metadata parameters are set (#10112 by Stefan Appelhoff)

• Fix bug with mne.Epochs where save-load round-trip with FIF would cause mne.Epochs.apply_baseline() to no longer work (#10177 by Eric Larson)

• Fix functions by adding missing overwrite parameters: mne.write_events(), mne.write_cov(), mne.write_evokeds(), mne.SourceEstimate.save(), mne.minimum_norm.write_inverse_operator(), mne.write_proj(), and related methods (#10127 by Eric Larson)

• Fix bug with mne.transforms.compute_volume_registration() and mne.compute_source_morph() (volumetric) where the smoothing factors were not scaled based on zooms (#10132 by Eric Larson)

• Remove repeated logging output when overwriting an existing Raw file (#10095 by Richard Höchenberger and Stefan Appelhoff)

• In the plots generated by mne.Report.add_stc(), we now only add 5 labels to the color bar to reduce the chance of overlap, which could previously cause the labels to become unreadable (#10135 by Richard Höchenberger)

• mne.Report.add_trans() now allows you to add sensor alignment plots for head surfaces that have topological defects (#10175 by Richard Höchenberger)

• mne.Report.add_trans() now also works if no digitization points are present in the data (#10176 by Jeff Stout)

• Argument verbose is now respected by dataset fetching (#10210 by Mathieu Scheltienne)

• Fix bug with mne.io.read_raw_hitachi() where empty Comment descriptions were not handled properly (#10235 by Eric Larson)

• Fix bug with input validation of low-level filtering functions (#10267 by Eric Larson)

• mne.gui.coregistration() now works with surfaces containing topological defects (#10230, by Richard Höchenberger)

• Fix bug with mne.io.read_raw_nirx() being unable to read measurement dates recorded on systems with German (de_DE), French (fr_FR), and Italian (it_IT) locales (#10277 by Eric Larson)

• Fix bug with projector normalization checks that were too sensitive, and improve warning (#10292 by Eric Larson)

• Fix bug with mne.viz.plot_alignment() where head-coordinate source spaces (e.g., from a forward solution) were not properly plotted (#10309 by Eric Larson)

• mne.read_trans() and mne.io.read_fiducials() now correctly expand ~ in the provided path (i.e., to the user’s home directory) (#10265, #10415, by Richard Höchenberger)

• mne.find_events() now uses first_samp and not 0 for initial event when using initial_value (#10289, by Alex Gramfort)

• Fix bug with mne.channels.make_standard_montage() for 'standard*', 'mgh*', and 'artinis*' montages where the points were incorrectly scaled and fiducials incorrectly set away from the correct values for use with the fsaverage subject (#10324 by Eric Larson)

• Fix bug with mne.Report.add_figure() where figures generated externally were closed and possibly resized during render (#10342 by Eric Larson)

• Fix bug with mne.viz.plot_sparse_source_estimates() where the return value was incorrect (#10347 by Eric Larson)

• Fix plotting bug in How to convert 3D electrode positions to a 2D image and make view look more natural in Annotate movement artifacts and reestimate dev_head_t (#10313, by Alex Rockhill)

• Fix bug with blank 3D rendering with MESA software rendering (#10400 by Eric Larson)

• Fix a bug in mne.gui.locate_ieeg where 2D lines on slice plots failed to update and were shown when not in maximum projection mode (#10335, by Alex Rockhill)

• Fix misleading color scale in Non-parametric between conditions cluster statistic on single trial power for the plotting of cluster F-statistics (#10393 by Alex Rockhill)

• Fix baseline removal using remove_dc=True in raw.plot() for data containing np.nan (#10392 by Clemens Brunner)

• Fix misleading color scale in Mass-univariate twoway repeated measures ANOVA on single trial power for plotting F-stats (#10401 by Alex Rockhill)

• Fix misleading T_obs return name for mne.stats.spatio_temporal_cluster_test() when the default returns an F-statistic (#10401 by Alex Rockhill)

API changes

• The default browser for raw.plot(), epochs.plot(), and ica.plot_sources() has been changed to the 'qt' backend on systems where mne_qt_browser is installed. To change back to matplotlib within a session, you can use mne.viz.set_browser_backend('matplotlib'). To set it permanently on your system, you can use mne.set_config('MNE_BROWSER_BACKEND', 'matplotlib') (#9960 by Martin Schulz and Eric Larson)

• mne.Info.pick_channels has been deprecated. Use inst.pick_channels to pick channels from Raw, Epochs, and Evoked. Use mne.pick_info() to pick channels from mne.Info (#10039 by Mathieu Scheltienne)

• All data_path functions now return pathlib.Path objects rather than strings. Support for string concatenation with plus (+) is thus deprecated and will be removed in 1.2, use the forward-slash / operator instead (#10348 by Eric Larson)

• Argument event_list has been deprecated in favor of events in mne.write_events() (#10056 by Mathieu Scheltienne)

• mne.preprocessing.annotate_flat has been deprecated in favor of mne.preprocessing.annotate_amplitude(), that covers both minimum and maximum peak-to-peak variation. (#10143 by Mathieu Scheltienne)

• The max_ori_out parameter of mne.beamformer.apply_lcmv() and related functions is being removed as only signed estimates are supported. abs(stc) can be used to obtain unsigned estimates (#10366 by Eric Larson)

• The verbose attribute of classes (e.g., mne.io.Raw, mne.Epochs, etc.) has been deprecated. Explicitly pass verbose to methods as necessary instead. (#10267 by Eric Larson)

• In mne.viz.set_browser_backend(), the mne-qt-browser-based backend is now called 'qt' rather than 'pyqtgraph' for simplicity (#10323 by Eric Larson)

Dependencies

Numerous external dependencies that used to be bundled with MNE-Python are now not shipped with the package anymore and will instead be retrieved automatically from their official sources when you install MNE-Python. This simplifies MNE-Python maintenance and keeps the package smaller. The following new dependencies have been added:

• Jinja2 (replaces Tempita, which is not maintained anymore; #10211 by Richard Höchenberger)

Authors

• Adam Li

• Adina Wagner+

• Alex Rockhill

• Alexandre Gramfort

• Britta Westner

• Clemens Brunner

• Daniel McCloy

• Eduard Ort

• Eric Larson

• Etienne de Montalivet+

• Federico Zamberlan+

• Guillaume Favelier

• Jan Sosulski

• Jan Zerfowski+

• Jeff Stout

• John Veillette+

• Joshua Teves

• Julia Guiomar Niso Galán

• Luke Bloy

• Marijn van Vliet

• Martin Schulz

• Mathieu Scheltienne

• Matthias Eberlein+

• Michiru Kaneda+

• Mikołaj Magnuski

• Nikolai Chapochnikov+

• Richard Höchenberger

• Robert Luke

• Scott Huberty+

• Senwen Deng+

• Stefan Appelhoff

• Steve Matindi

• Thomas Hartmann