What’s new

Current (1.4.dev0)

Enhancements

• Add :unit: Sphinx directive to enable use of uniform non-breaking spaces throughout the documentation (#11469 by new contributor Sawradip Saha)

• Adjusted the algorithm used in mne.decoding.SSD to support non-full rank data (#11458 by new contributor Thomas Binns)

• Changed suggested type for ch_groups` in mne.viz.plot_sensors from array to list of list(s) (arrays are still supported). (#11465 by Hyonyoung Shin)

• Add support for UCL/FIL OPM data using mne.io.read_raw_fil() (#11366 by new contributor George O’Neill and Robert Seymour)

• Forward argument axes from mne.viz.plot_sensors to mne.channels.DigMontage.plot (#11470 by new contributor Jan Ebert and Mathieu Scheltienne)

• Add forward IIR filtering, using parameters method='iir', phase='forward' (#11078 by new contributor Quentin Barthélemy)

• Added ability to read stimulus durations from SNIRF files when using mne.io.read_raw_snirf() (#11397 by Robert Luke)

• Add mne.Info.save() to save an mne.Info object to a fif file (#11401 by Alex Rockhill)

• Improved error message when downloads are corrupted for mne.datasets.sample.data_path() and related functions (#11407 by Eric Larson)

• Add support for skip_by_annotation in mne.io.Raw.notch_filter() (#11388 by Mainak Jas)

• Add support for output='complex' to mne.time_frequency.psd_array_welch() and when using method='welch' with mne.Epochs.compute_psd() (#11556 by Eric Larson)

• Slightly adjusted the window title for mne.Epochs.plot() (#11419 by Richard Höchenberger and Daniel McCloy)

• Add mne.count_events() to count unique event types in a given event array (#11430 by Clemens Brunner)

• Add a video to How MNE uses FreeSurfer’s outputs of a brain inflating from the pial surface to aid in understanding the inflated brain (#11440 by Alex Rockhill)

• Add automatic projection of sEEG contact onto the inflated surface for mne.viz.Brain.add_sensors() (#11436 by Alex Rockhill)

• Allow an image with intracranial electrode contacts (e.g. computed tomography) to be used without the freesurfer recon-all surfaces to locate contacts so that it doesn’t have to be downsampled to freesurfer dimensions (for microelectrodes) and show an example Locating micro-scale intracranial electrode contacts with mne.transforms.apply_volume_registration_points() added to aid this transform (#11567 by Alex Rockhill)

• Use new dipy.workflows.align.DiffeomorphicMap.transform_points() to transform a montage of intracranial contacts more efficiently (#11572 by Alex Rockhill)

• Add support for eyetracking data using mne.io.read_raw_eyelink() (#11152 by Dominik Welke and Scott Huberty)

Bugs

• Fix mne.time_frequency.psd_array_multitaper() docstring where argument bandwidth incorrectly reported argument as half-bandwidth and gave wrong explanation of default value (#11479 by :newcontrib: Tom Stone)

• Fix bug where installation of a package depending on mne will error when done in an environment where setuptools is not present (#11454 by :newcontrib: Arne Pelzer)

• Fix bug where mne.preprocessing.regress_artifact() and mne.preprocessing.EOGRegression incorrectly tracked picks (#11366 by Eric Larson)

• Fix bug where channel names were not properly sanitized in mne.write_evokeds() and related functions (#11399 by Eric Larson)

• Fix bug where splash screen would not always disappear (#11398 by Eric Larson)

• Fix bug where having a different combination of volumes loaded into freeview caused different affines to be returned by mne.read_lta() for the same Linear Transform Array (LTA) (#11402 by Alex Rockhill)

• Fix how mne.channels.DigMontage is set when using mne.gui.locate_ieeg() so that mne.Info.get_montage() works and does not return None (#11421 by Alex Rockhill)

• Fix mne.io.read_raw_edf() when reading EDF data with different sampling rates and a mix of data channels when using infer_types=True (#11427 by Alex Gramfort)

• Fix how mne.channels.DigMontage is set when using mne.preprocessing.ieeg.project_sensors_onto_brain() so that mne.Info.get_montage() works and does not return None (#11436 by Alex Rockhill)

• Fix configuration folder discovery on Windows, which would fail in certain edge cases; and produce a helpful error message if discovery still fails (#11441 by Richard Höchenberger)

• Make SlidingEstimator and GeneralizingEstimator respect the verbose argument. Now with verbose=False, the progress bar is not shown during fitting, scoring, etc. (#11450 by Mikołaj Magnuski)

• Fix bug with mne.gui.locate_ieeg() where Freesurfer ?h.pial.T1 was not recognized and suppress excess logging (#11489 by Alex Rockhill)

• All functions accepting paths can now correctly handle Path as input. Historically, we expected strings (instead of “proper” path objects), and only added Path support in a few select places, leading to inconsistent behavior. (#11473 and #11499 by Mathieu Scheltienne)

• Fix visualization dialog compatibility with matplotlib 3.7 (#11409 by Daniel McCloy and Eric Larson)

• Expand tilde (user directory) in config keys (#11537 by Clemens Brunner)

• Fix bug in mne.preprocessing.compute_maxwell_basis() where using int_order=0 would raise an error (#11562 by Eric Larson)

• In the legacy function mne.viz.plot_epochs_psd_topomap(), the parameter names now works again (#11563 by Daniel McCloy)

• Fix mne.io.read_raw() for file names containing multiple dots (#11521 by Clemens Brunner)

• Fix bug in mne.export.export_raw() when exporting to EDF with a physical range set smaller than the data range (#11569 by Mathieu Scheltienne)

• Fix bug in mne.concatenate_raws() where two raws could not be merged if the order of the bad channel lists did not match (#11502 by Moritz Gerster)

• Fix bug where mne.Evoked.plot_topomap() opened an extra figure (#11607 by Alex Rockhill)

API changes

• Deprecate arguments kind and path from mne.channels.read_layout() in favor of a common argument fname (#11500 by Mathieu Scheltienne)

• Change aligned_ct positional argument in mne.gui.locate_ieeg() to base_image to reflect that this can now be used with unaligned images (#11567 by Alex Rockhill)

• mne.warp_montage_volume was deprecated in favor of mne.preprocessing.ieeg.warp_montage() (acts directly on points instead of using an intermediate volume) and mne.preprocessing.ieeg.make_montage_volume() (which makes a volume of ieeg contact locations which can still be useful) (#11572 by Alex Rockhill)

Version 1.3.1 (2023-02-23)

Bugs

• Fix visualization dialog compatibility with matplotlib 3.7 (#11409 by Daniel McCloy and Eric Larson)

Version 1.3.0 (2022-12-21)

Enhancements

• Improve default line width used in mne.viz.plot_filter() (#11333 by new contributor Toomas Erik Anijärv)

• Add the argument max_iter to psd_array_multitaper() and to csd_array_multitaper() to increase the maximum number of iterations to reach convergence when using adaptive=True (#11237 by Mathieu Scheltienne)

• Add a warning to the docstring of mne.channels.find_ch_adjacency() to encourage users to validate their outputs (#11236 by Felix Klotzsche and Eric Larson)

• Mixed, cortical + discrete source spaces with fixed orientations are now allowed. (#11241 by Jevri Hanna)

• Add size information to the repr of mne.Report (#11357 by Eric Larson)

• Add support for image_format='webp' to mne.Report when using Matplotlib 3.6+, which can reduce file sizes by up to 50% compared to 'png'. The new default image_format='auto' will automatically use this format if it’s available on the system (#11359 by Eric Larson)

• Add mne.beamformer.apply_dics_tfr_epochs() to apply a DICS beamformer to time-frequency resolved epochs (#11096 by Alex Rockhill)

• Add mne.time_frequency.fwhm() to determine the full-width half maximum for mne.time_frequency.morlet() (#11353 by Britta Westner, Daniel McCloy, and Eric Larson)

• Check whether head radius (estimated from channel positions) is correct when reading EEGLAB data with read_raw_eeglab() and read_epochs_eeglab(). If head radius is not within likely values, warn informing about possible units mismatch and the new montage_units argument (#11283 by Mikołaj Magnuski).

• Add support for a callable passed in combine for mne.time_frequency.AverageTFR.plot and mne.time_frequency.AverageTFR.plot_joint (#11329 by Mathieu Scheltienne)

Bugs

• Fix bug in mne.export.export_raw() when exporting raw to EDF with EDFLib when subject sex is missing (#11375 by new contributor Mark Alexander Henney)

• Fix bugs in documentation of mne.time_frequency.tfr_array_multitaper() and related functions/methods (#11310 by new contributor Santeri Ruuskanen)

• Fix bug to be able to customize legends when using mne.viz.Brain.add_volume_labels() (#11289 by new contributor Mauricio Cespedes Tenorio)

• Fix bug in documentation of mne.channels.make_dig_montage() (#11235 by new contributor Daniel Hasegan)

• Add support for bad channel handling in mne.set_bipolar_reference() (#11245 by Moritz Gerster, new contributor Dinara Issagaliyeva, new contributor Jennifer Behnke, new contributor Hakimeh Aslsardroud, and new contributor Pavel Navratil)

• Fix X coordinates of ear_left and ear_right in head outlines dict (#11255 by new contributor Tom Ma)

• Add type checking for tmin and tmax arguments for crop (#11263 by new contributor Carlos de la Torre-Ortiz).

• Fix bug where trying to setup projection without an EEG average reference projector would fail (#11351 by new contributor Enzo Altamiranda)

• Fix bug where ica.reject_ was not saved to disk, and the ica.reject_ property was not inherited from Epochs when doing ICA.fit(epochs) (#11244 by Eric Larson)

• Fix bug in automatic MESA detection for disabling advanced 3D options (#11271 by Eric Larson)

• Fix bug in mne.head_to_mri() when unscale=True (#11303 by Eric Larson)

• Fix bug in set_montage('mgh60') and related functions where the 'mgh60' sensor positions were incorrectly ordered (#11290 by Eric Larson)

• Fix bug in the .compute_psd() methods where the number of unaggregated Welch segments was wrongly computed for some inputs, leading to an assertion error when computing the PSD (#11248 by Daniel McCloy)

• Fix bug in the plot_evoked_topo() and plot_topo(), where legend colors where shown incorrectly on newer matplotlib versions (#11258 by Erkka Heinila)

• Fix bug where EEGLAB channel positions were read as meters, while they are commonly in millimeters, leading to head outlies of the size of one channel when plotting topomaps. Now montage_units argument has been added to read_raw_eeglab() and read_epochs_eeglab() to control in what units EEGLAB channel positions are read. The default is millimeters, 'mm' (#11283 by Mikołaj Magnuski)

• Fix bug where computing PSD with welch’s method with more jobs than channels would fail (#11298 by Mathieu Scheltienne)

• Fix bug where the default FFT length changed for spectrum plots (#11345 by Daniel McCloy)

• Fix bug with mne.decoding.cross_val_multiscore() where progress bars were not displayed correctly (#11311 by Eric Larson)

• Fix channel selection edge-cases in find_bads_muscle (#11300 by Mathieu Scheltienne)

• Fix bug with mne.io.read_raw_curry() where a dot in the parent folders prevented files from being read (#11340 by Eric Larson)

• Fix bug with mne.Report with replace=True where the wrong content was replaced and section was not respected (#11318, #11346 by Eric Larson)

• Fix bug with unit conversion when setting reference MEG as the channel type in mne.io.Raw.set_channel_types() and related methods (#11344 by Eric Larson)

• Fix bug where reference MEG channels could not be plotted using mne.viz.plot_epochs_image() (#11344 by Eric Larson)

• Fix bug where image_format='gif' was errantly documented as being supported by mne.Report, it is now only supported in mne.Report.add_image() (#11347 by Eric Larson)

• Multitaper spectral estimation now uses periodic (rather than symmetric) taper windows. This also necessitated changing the default max_iter of our cross-spectral density functions from 150 to 250. (#11293 by Daniel McCloy)

• Fix mne.Epochs.plot_image() and mne.viz.plot_epochs_image() when using EMG signals (#11322 by Alex Gramfort)

• Fix selection of ICA components in mne.viz.plot_ica_components() and mne.preprocessing.ICA.plot_components() (#11369 by Mathieu Scheltienne)

• Fix bug where a Freesurfer reconstruction run with both a T1 and a T2 caused mne.viz.Brain not to initialize pial surfaces properly (#11361 by Alex Rockhill)

API changes

• In mne.time_frequency.dpss_windows(), interpolating is deprecated (nowadays SciPy’s computations are fast enough for large N without interpolation). This affects parameters interp_from and interp_kind. Two new parameters of the underlying SciPy dpss() function are also exposed: sym (for choosing symmetric vs. periodic windows) and norm (window normalization method). (#11293 by Daniel McCloy)

• In mne.decoding.CSP.plot_patterns(), mne.decoding.CSP.plot_filters(), mne.preprocessing.ICA.plot_components(), and mne.viz.plot_ica_components(), the parameters vmin and vmax are deprecated in favor of vlim, for consistency with other topomap-plotting functions and methods (#11371 by Daniel McCloy)

• In mne.decoding.CSP.plot_patterns() and mne.decoding.CSP.plot_filters() the title parameter is deprecated and will be removed in version 1.4 (#11371 by Daniel McCloy)

• The APIs of mne.preprocessing.ICA.plot_components() and mne.viz.plot_ica_components() gained new parameters show_names, extrapolate, border, size, cnorm, cbar_fmt, axes, nrows, ncols, for consistency with other topomap-plotting functions and methods (#11371 by Daniel McCloy)

• The APIs of mne.decoding.CSP.plot_patterns() and mne.decoding.CSP.plot_filters() gained new parameters extrapolate, border, cnorm, axes, nrows, ncols, for consistency with other topomap-plotting functions and methods (#11371 by Daniel McCloy)

Authors

• Alex Rockhill

• Alexandre Gramfort

• Britta Westner

• Carlos de la Torre+

• Daniel Hasegan+

• Daniel McCloy

• Dinara Issagaliyeva+

• Enzo Altamiranda+

• Eric Brayet+

• Eric Larson

• Erkka Heinila

• Felix Klotzsche

• Hakimeh Aslsardroud+

• Jennifer Behnke+

• Jevri Hanna

• Lukas Hecker

• Mark Alexander Henney+

• Mathieu Scheltienne

• Mauricio Cespedes+

• Mikołaj Magnuski

• Moritz Gerster

• Omer Shubi+

• Pavel Navratil+

• Richard Höchenberger

• Santeri Ruuskanen+

• Stefan Appelhoff

• Timon Merk

• Tom Ma+

• Toomas Erik Anijärv+

Version 1.2.0 (2022-10-11)

Enhancements

• Add vmin and vmax parameters to mne.Evoked.animate_topomap() (#11073 by new contributor Mats van Es)

• Enable common average reference projection for ECoG, sEEG, and DBS data (optionally jointly with joint=True) in set_eeg_reference() and related functions/methods (#10656 by new contributor Moritz Gerster and Eric Larson)

• The trans parameter in mne.make_field_map() now accepts a Path object, and uses standardised loading logic (#10784 by new contributor Andrew Quinn)

• Add support for computing forward solutions using OpenMEEG (#11011 by Alex Gramfort and Eric Larson)

• EEGLAB files (saved as MAT versions less than v7.3) can now be imported with mne.io.read_raw_eeglab() without the optional dependency pymatreader (#11006 by Clemens Brunner)

• Add eight source estimate comparison metrics to new submodule mne.simulation.metrics (#6233 by Kostiantyn Maksymenko and Alex Gramfort)

• Add mne.time_frequency.csd_tfr() to compute cross-spectral density from mne.time_frequency.EpochsTFR (#10986 by Alex Rockhill)

• Improve repr() for mne.minimum_norm.InverseOperator when loose orientation is used (#11048 by Eric Larson)

• Add support for vector and volume source estimates in mne.minimum_norm.get_point_spread() and mne.minimum_norm.get_cross_talk() (#8639, #11083 by Olaf Hauk, Marijn van Vliet, Alex Gramfort, and Eric Larson)

• mne.Epochs.plot_psd_topomap() now suppresses redundant colorbars when vlim='joint' (#11051 by Daniel McCloy)

• Add starting_affine keyword argument to mne.transforms.compute_volume_registration() to initialize an alignment with an affine (#11020 by Alex Rockhill)

• Add HTML representation for Evoked in Jupyter Notebooks (#11075 by Valerii Chirkov and Andrew Quinn)

• Add support for temperature and gsr (galvanic skin response, i.e., electrodermal activity) channel types (#11090, #11108 by Eric Larson and Richard Höchenberger)

• Allow mne.beamformer.make_dics() to take pick_ori='vector' to compute vector source estimates (#19080 by Alex Rockhill)

• Add units parameter to mne.io.read_raw_edf() in case units are missing from the file (#11099 by Alex Gramfort)

• Add on_missing functionality to all of our classes that have a drop_channels method, to control what happens when channel names are not in the object (#11077 by Andrew Quinn)

• Improve interpolation of bridged electrodes with interpolate_bridged_electrodes (#11094 by Mathieu Scheltienne)

• Add mne.minimum_norm.apply_inverse_tfr_epochs() to apply inverse methods to time-frequency resolved epochs (#11095 by Alex Rockhill)

• Add support for multiple probes via multiple CSV files passed to mne.io.read_raw_hitachi() (#11186 by Eric Larson)

• Add mne.chpi.get_active_chpi() to retrieve the number of active hpi coils for each time point (#11122 by Eduard Ort)

• Add example of how to obtain time-frequency decomposition using narrow bandpass Hilbert transforms to Time-frequency on simulated data (Multitaper vs. Morlet vs. Stockwell vs. Hilbert) (#11116 by Alex Rockhill)

• Add == and != comparison between mne.Projection objects (#11147 by Mathieu Scheltienne)

• Parse automatically temperature channel with mne.io.read_raw_edf() (#11150 by Eric Larson and Alex Gramfort)

• Add unscale option to mne.head_to_mri() to facilitate working with surrogate MRI data (#11185 by Eric Larson)

• Add encoding parameter to mne.io.read_raw_edf() and mne.io.read_raw_bdf() to support custom (non-UTF8) annotation channel encodings (#11154 by Clemens Brunner)

• mne.preprocessing.ICA gained a new method, get_explained_variance_ratio(), that allows the retrieval of the proportion of variance explained by ICA components (#11141 by Richard Höchenberger)

• Add on_baseline to mne.preprocessing.ICA.apply(), mne.preprocessing.ICA.plot_overlay(), and mne.viz.plot_ica_overlay() to allow reapplying baseline correction after applying ICA (#11232 by Eric Larson)

• Add config option MNE_REPR_HTML to disable HTML repr in notebook environments (#11159 by Clemens Brunner)

Bugs

• Fix bug in mne.io.Raw.crop() where argument include_tmax was not considered in checking tmax in bounds (#11196 by Lukas Gemein)

• Fix bug in mne.io.read_raw_eeglab() where unlabeled fiducials caused reading errors (#11074 by new contributor Sebastiaan Mathot)

• Fix bug in mne.time_frequency.read_csd() that returned projs as a list of dict instead of mne.Projection (#11072 by new contributor Chetan Gohil)

• Fix bug in mne.decoding.TimeFrequency() that prevented cloning if constructor arguments were modified (#11004 by new contributor Daniel Carlström Schad)

• Fix bug in repr of decoding estimator classes (e.g., mne.decoding.SlidingEstimator) where the parameters where not stored in the result string but instead just printed to sys.stdout (#11190 by new contributor Dominik Wetzel)

• Document height and weight keys of subject_info entry in mne.Info (#11019 by new contributor Sena Er)

• Fix bug in mne.viz.Brain constructor where the first argument was named subject_id instead of subject (#11049 by Eric Larson)

• Fix bug in mne coreg where the MEG helmet position was not updated during ICP fitting (#11084 by Eric Larson)

• Fix bug in read_raw_curry(), and read_raw_cnt() where digitization points were not read properly (#11145 by Eric Larson)

• Fix bug in mne.minimum_norm.apply_inverse_epochs() where the average EEG projector was not checked properly (#11182 by Eric Larson)

• Fix bug in mne.viz.plot_filter() when plotting filters created using output='ba' mode with compensation turned on. (#11040 by Marian Dovgialo)

• Fix bugs in documentation of surface SourceSpaces (#11171 by Eric Larson)

• Fix bug in mne.viz.plot_compare_evokeds() where automatic legend labels could be excessively long; they are now abbreviated with ... when necessary (#11181 by Eric Larson)

• Fix bugs with verbose='error' not being used properly and allowing warnings through (#11193 by Eric Larson)

• Fix bug in mne.io.read_raw_bti() where EEG, EMG, and H/VEOG channels were not detected properly, and many non-ECG channels were called ECG. The logic has been improved, and any channels of unknown type are now labeled as misc (#11102 by Eric Larson)

• Fix bug in mne.viz.plot_topomap() when providing sphere="eeglab" (#11081 by Mathieu Scheltienne)

• Fix bug in mne.Dipole.to_mri() where MRI RAS rather than MRI surface RAS was returned (#11185 by Eric Larson)

• Fix bug in epochs.save where the verbose parameter defaulted to True instead of None (#11191 by Eric Larson)

• The string and HTML representation of mne.preprocessing.ICA reported incorrect values for the explained variance. This information has been removed from the representations, and should instead be retrieved via the new get_explained_variance_ratio() method (#11141 by Richard Höchenberger)

• Fix bug in mne.Evoked.plot() and related methods where a np.nan location value in any channel causes spatial colours to fail (#6870 by Simeon Wong)

• Fix bug in mne.preprocessing.ICA.find_bads_muscle() where epochs caused an error when passed as the inst (#11197 by Alex Rockhill)

• Fix bug in readers where EEG coordinates were assumed to be in head coordinates but no fiducial points were present. Estimated fiducial locations will now be added automatically to reflect the assumption of locations being in the head coordinate frame (#11212 by Stefan Appelhoff and Eric Larson)

• The duration of raw data sometimes wasn’t displayed correctly in Jupyter notebooks by omitting fractions of a second. We now always round up to the next full second so a duration of less than 1 second will not be displayed as a duration of zero anymore (#11203 by Richard Höchenberger)

• Fix bug in mne.Report.add_ica() and where baselines were not reapplied to the data when inst is Epochs or Evoked (#11232 by Eric Larson)

API changes

• In meth:mne.Evoked.plot, the default value of the spatial_colors parameter has been changed to 'auto', which will use spatial colors if channel locations are available (#11201 by new contributor Hüseyin Orkun Elmas and Daniel McCloy)

• Starting with this release we now follow the Python convention of using FutureWarning instead of DeprecationWarning to signal user-facing changes to our API (#11120 by Daniel McCloy)

• The names parameter of mne.viz.plot_arrowmap() and mne.viz.plot_regression_weights() has been deprecated; sensor names will be automatically drawn from the info_from or model parameter (respectively), and can be hidden, shown, or altered via the show_names parameter (#11123 by Daniel McCloy)

• The bands parameter of mne.Epochs.plot_psd_topomap() now accepts dict input; legacy tuple input is supported, but discouraged for new code (#11050 by Daniel McCloy)

• The mne.head_to_mri() new function parameter kind default will change from 'ras' to 'mri' (#11185 by Eric Larson)

• The show_toolbar argument to mne.viz.Brain is being removed by deprecation (#11049 by Eric Larson)

• New classes Spectrum and EpochsSpectrum, created via new methods Raw.compute_psd(), Epochs.compute_psd(), and Evoked.compute_psd() (#10184 by Daniel McCloy)

• Functions/methods for plotting topomaps now have more consistent signatures; most have gained parameters for finer control of the topomap image and/or colorbar. See docstrings for details (#11123 by Daniel McCloy)

• In mne.viz.plot_topomap(), passing axes=None will now create a new Figure instead of plotting into the current axes (#11123 by Daniel McCloy)

• In mne.viz.plot_topomap(), the parameter show_names has been deprecated, use the names parameter instead (#11123 by Daniel McCloy)

• In mne.viz.plot_topomap(), plot_tfr_topomap(), plot_evoked_topomap(), and related class methods mne.Covariance.plot_topomap(), mne.Evoked.plot_topomap(), and mne.time_frequency.AverageTFR.plot_topomap(): the parameters vmin and vmax are deprecated in favor of vlim, for consistency with other plot_topomap functions and methods (#11123 by Daniel McCloy)

• In mne.viz.plot_tfr_topomap(), plot_evoked_topomap(), and related class methods mne.Covariance.plot_topomap(), mne.Evoked.plot_topomap(), and mne.time_frequency.AverageTFR.plot_topomap(): the title parameter has been deprecated; use matplotlib’s fig.suptitle() instead (#11123 by Daniel McCloy)

• In functions/methods for plotting topomaps, the outlines='skirt' option is deprecated; use sphere='eeglab' for similar functionality (#11123 by Daniel McCloy)

• The mne.epochs.add_channels_epochs function has been deprecated in favor of epochs.add_channels (#11180 by Eric Larson)

• The PSD functions that operate on Raw/Epochs/Evoked instances (mne.time_frequency.psd_welch and mne.time_frequency.psd_multitaper) are deprecated; for equivalent functionality create Spectrum or EpochsSpectrum objects instead and then run spectrum.get_data(return_freqs=True) (#10184 by Daniel McCloy)

• Added new class mne.preprocessing.EOGRegression to allow more flexibility when using regression to reduce EOG artifacts (#11046 by Marijn van Vliet)

• New parameter exclude added to mne.preprocessing.regress_artifact() to prevent regression from being applied to certain channels (#11046 by Marijn van Vliet)

Authors

• Alex Rockhill

• Alexandre Gramfort

• Andrew Quinn+

• Chetan Gohil+

• Christian Brodbeck

• Clemens Brunner

• Daniel Carlström Schad+

• Daniel McCloy

• Dominik Wetzel+

• Eduard Ort

• Eric Larson

• Hüseyin Orkun Elmas+

• Jack Zhang

• Joan Massich

• Julius Welzel+

• Kostiantyn Maksymenko

• Lukas Gemein

• Marian Dovgialo

• Marijn van Vliet

• Mathieu Scheltienne

• Mats van Es+

• Moritz Gerster+

• Olaf Hauk

• Richard Höchenberger

• Sebastiaan Mathot+

• Sena Er+

• Simeon Wong

• Stefan Appelhoff

• Valerii Chirkov

• luzpaz+

Version 1.1.0 (2022-08-03)

Enhancements

• Added new built-in montage R-Net 128 Ch (Brain Products) (#10974 by new contributor Ilias Machairas)

• DigMontage objects can now be checked for equality via == (#10942 by new contributor Tziona NessAiver)

• Add a note to clarify the inclusion of average referencing gain matrix during whitening (#10922 by new contributor Mingjian He)

• Add time axis scale bar for mne.Epochs.plot() using matplotlib backend (#10736 by new contributor Jordan Drew)

• Add mne.bem.distance_to_bem() to find depth of source positions (#10632 by new contributor Matt Courtemanche)

• Add support for ahdr files in mne.io.read_raw_brainvision() (#10515 by new contributor Alessandro Tonin)

• Add support for reading data from Gowerlabs devices to mne.io.read_raw_snirf() (#10555 by new contributor Samuel Powell and Robert Luke)

• Add built-in sensor layout files for Geodesic Head Web 130 and 280 devices (#10627 by Evan Hathaway)

• Add mne-icalabel to mne.sys_info() (#10615 by Adam Li)

• Add support for overview_mode in raw.plot() and related functions/methods (#10501 by Eric Larson)

• Add mne.io.Raw.crop_by_annotations() method to get chunks of Raw data based on mne.Annotations. (#10460 by Alex Gramfort)

• The pick_channels method gained a verbose parameter, allowing e.g. to suppress messages about removed projectors (#10544 by Richard Höchenberger)

• Add mne.viz.plot_projs_joint() for joint plotting of projectors and Evoked (#10720 by Eric Larson)

• The mne.make_forward_dipole() function can now take a list of dipoles to make a multi-dipole forward models (#10464 by Marijn van Vliet)

• Add mode='outlines' support to mne.Dipole.plot_locations() and mne.viz.plot_dipole_locations() (#10699 by Eric Larson)

• Add mne.preprocessing.ICA.find_bads_muscle() to find muscle-related ICA components with an example, Removing muscle ICA components (#10534 by Alex Rockhill)

• Add example of Xfit-style ECD modeling using multiple dipoles (#10464 by Marijn van Vliet)

• Add head_source argument to mne.make_field_map() to allow selecting which head source to use (#10568 by Eric Larson)

• Add support for n_jobs=None to support joblib.parallel_backend() for more precise control over parallelization (#10567 by Eric Larson)

• It is now possible to compute inverse solutions with restricted source orientations using discrete forward models (#10464 by Marijn van Vliet)

• The new function mne.preprocessing.maxwell_filter_prepare_emptyroom() simplifies the preconditioning of an empty-room recording for our Maxwell filtering operations (#10533 by Richard Höchenberger and Eric Larson)

• Add keyboard shortcuts to toggle mne.preprocessing.ICA.plot_properties() topomap channel types (‘t’) and power spectral density log-scale (‘l’) (#10557 by Alex Rockhill)

• Add --mri, and --threshold options to mne make_scalp_surfaces to improve head surface mesh extraction (#10591 by Eric Larson)

• Add mne.preprocessing.compute_bridged_electrodes() to detect EEG electrodes with shared spatial sources due to a conductive medium connecting two or more electrodes, add Identify EEG Electrodes Bridged by too much Gel for an example and mne.viz.plot_bridged_electrodes() to help visualize (#10571 by Alex Rockhill)

• Add 'nearest' as an option for the image_interp argument in mne.viz.plot_topomap() to plot a topomap without interpolation using a Voronoi parcelation (#10571 by Alex Rockhill)

• Add mne.preprocessing.interpolate_bridged_electrodes() to use the spatially smeared signal to get a better interpolation rather than dropping those channels (#10587 by Alex Rockhill)

• Add support for hemoglobin type fNIRS data to temporal derivative distribution repair (TDDR) mne.preprocessing.nirs.temporal_derivative_distribution_repair() (#10125 by Johann Benerradi)

• mne.viz.plot_evoked_topomap() and mne.Evoked.plot_topomap() now display the time range the map was averaged over if average was passed (#10606 by Richard Höchenberger)

• mne.viz.plot_evoked_topomap() and mne.Evoked.plot_topomap() can now average the topographic maps across different time periods for each time point. To do this, pass a list of periods via the average parameter (#10610 by Richard Höchenberger)

• mne.viz.plot_evoked() and mne.Evoked.plot() gained a new parameter, highlight, to visually highlight time periods of interest (#10614 by Richard Höchenberger)

• Added fNIRS support to mne.Info.get_montage() (#10611 by Robert Luke)

• Add mne.viz.plot_ch_adjacency() to visualize and manually edit the channel adjacency matrix (#10633 by Mikołaj Magnuski)

• Add mne.viz.Brain.get_view() to get the current camera parameters such that they can be passed to mne.viz.Brain.show_view() (#10661 by Alex Rockhill)

• Added support for Aurora version 2021.9.0.6 to mne.io.read_raw_nirx() (#10668 by Robert Luke)

• Added BrainVision format (.vhdr, .vmrk, .eeg) to mne.export.export_raw() (#10681 by Stefan Appelhoff)

• Added export method to mne.Evoked (#10681 by Stefan Appelhoff)

• Add timeformat YYYY/MM/DD to mne.io.ctf.info._convert_time (#10674 by Simon Kern)

• mne.Report.add_figure() and mne.Report.add_image() gained a new parameter, section, allowing to put multiple figures or images into the same “content block”. Previously, the only way to group figures and images was by means of a slider, which sometimes made content hard to discover. The slider remains available as an alternative (#10694 by Richard Höchenberger)

• All functions and methods that plot topographic maps for EEG (2D projections of the EEG sensor locations) now accept the parameter value sphere='eeglab' to lay out the sensors with respect to the head circle in a similar way to how EEGLAB does, i.e., T7/T8 and Fpz/Oz are placed directly on the circle for template montages (#10572 by Richard Höchenberger)

• mne.channels.get_builtin_montages() gained a new parameter, descriptions, which allows to retrieve the descriptions of the montages in addition to their names (#10373 by Richard Höchenberger)

• Add include option to mne.io.read_raw_edf(), mne.io.read_raw_bdf() and mne.io.read_raw_gdf(). (#10734 by Michiru Kaneda)

• mne.gui.coregistration() gained a new parameter, fullscreen, to start the GUI in fullscreen mode (#10284 by Richard Höchenberger)

• The built-in FieldTrip channel adjacency matrices, which can be read via read_ch_adjacency(), have been synchronized with FieldTrip again. This means that numerous new adjacencies have been added, most notably those for standard 10-05 and 10-20 montages (#10749 by Richard Höchenberger)

• mne.Evoked.plot_field() gained a new parameter, interaction, to control the rotation axes when interacting with the head (#10788 by Richard Höchenberger)

• Add mne.read_evoked_besa() for reading evokeds from BESA .avr and .mul files. (#10892 by Marijn van Vliet)

• Add mne.time_frequency.EpochsTFR.decimate() to reduce size of time-frequency epochs objects (#10940 by Alex Rockhill)

• Add an alias that maps EGI reference channel names (VREF or Vertex Reference) to the electrode name in the standard EGI montages (Cz). Now setting standard EGI montages with set_montage() with match_alias=True will avoid raising an error (#10823 by Scott Huberty)

• Add provenance in mne.time_frequency.EpochsTFR.apply_baseline() (#10979 by Alex Rockhill)

Bugs

• Fix bug in mne.surface._project_onto_surface for the condition method != 'accurate' and return_nn (#10930 by Christian O’Reilly)

• Fix bug in mne.export.export_raw() to ignore None value in filenames attribute of mne.io.RawArray (#10927 by new contributor Reza Nasri)

• Fix bug in mne.io.read_raw_edf() to allow reading in all Hypnodyne ZMax EDFs to be read in without issues (#10754 by new contributor Frederik Weber)

• Fix bug in mne.Epochs.drop_bad() where data was loaded although no rejection had to be performed (#10718 by new contributor Lukas Gemein)

• Pick also bad channels when selecting T1T2 magnetometers in mne.preprocessing.maxwell_filter() (#10639 by new contributor Matti Toivonen)

• Make color parameter check in in mne.viz.plot_evoked_topo() consistent (#10217 by new contributor T. Wang and Stefan Appelhoff)

• Fix bug in mne.io.read_raw_brainvision() when BrainVision data are acquired with the Brain Products “V-Amp” amplifier and disabled lowpass filter is marked with value 0 (#10517 by new contributor Alessandro Tonin)

• Fix bug in mne.pick_types() and related methods where csd=True was not passed handled properly (#10470 by new contributor Matthias Dold)

• Fix bug where plots produced using the 'qt' / mne_qt_browser backend could not be added using mne.Report.add_figure() (#10485 by Eric Larson)

• Fix bug where theme was not handled properly in mne.io.Raw.plot() (#10487, #10500 by Mathieu Scheltienne and Eric Larson)

• Fix bug in raw.crop(start, stop) that would cause annotations to be erroneously shifted when start != 0 and no measurement date was set. (#10491 by Eric Larson)

• Fix bug in mne.io.read_raw_bti() where unknown electrode locations were not handled properly (#10662 by Eric Larson)

• Fix bug in mne.io.read_raw_ctf() on Windows where large files could not be read (#10866 by Eric Larson)

• Fix bug in mne.io.read_raw_ctf() where invalid measurement dates were not handled properly (#10957 by Jean-Remi King and Eric Larson)

• Rendering issues with recent MESA releases can be avoided by setting the new environment variable``MNE_3D_OPTION_MULTI_SAMPLES=1`` or using mne.viz.set_3d_options() (#10513 by Eric Larson)

• Fix behavior for the pyvista 3D renderer’s quiver3D function so that default arguments plot a glyph in arrow mode (#10493 by Alex Rockhill)

• Retain epochs metadata when using mne.channels.combine_channels() (#10504 by Clemens Brunner)

• Fix epochs indexing with metadata containing boolean type and missing values (#10705 by Clemens Brunner and Alex Gramfort)

• Fix reading of fiducial locations in mne.io.read_raw_eeglab() (#10521 by Alex Gramfort)

• Prevent creation of montage with invalid [x, y, z] coordinates with mne.channels.make_dig_montage() (#10547 by Mathieu Scheltienne)

• Fix bug in coregistration GUI that prevented it from starting up if only a high-resolution head model was available (#10543 by Richard Höchenberger)

• Fix bug with mne.Epochs.add_reference_channels where attributes were not updated properly so subsequent pick_types calls were broken (#10912 by Eric Larson)

• Fix bug in the mne.viz.Brain tool bar that prevented the buttons to call the corresponding feature (#10560 by Guillaume Favelier)

• Fix issue with saving epochs once compute_current_source_density() has been used if a rejection threshold was used first (#10619 by Alex Rockhill and Richard Höchenberger)

• Fix bug in mne.viz.plot_evoked_image() that would cause incorrect sub-titles when using group_by (#10618 by Reza Shoorangiz)

• Reduce memory usage when loading an EDF file with preload=False (#10638 by Clemens Brunner)

• Fix bug in mne.io.Raw.get_channel_types() and related methods where unique=True would return a set with arbitrary order rather than a list that preserves the same order as inst.ch_names (#10720 by Eric Larson)

• In mne.preprocessing.find_bad_channels_maxwell(), do not re-filter the data if a low-pass filter with the requested frequency has already been applied (#10664 by Richard Höchenberger)

• Fix a problem in mne.Evoked.get_peak(), where under certain circumstances the mode parameters 'pos' and 'neg' were not honored when tmin and/or tmax were passed as well (#10686 by Richard Höchenberger)

• mne.read_evokeds(), mne.channels.read_custom_montage(), mne.channels.read_dig_hpts(), mne.channels.read_dig_polhemus_isotrak(), and mne.channels.read_polhemus_fastscan() now correctly expand ~ in the provided path to the user’s home directory (#10685, #10688 by Richard Höchenberger)

• Fix bug in mne.io.read_raw_eeglab() and mne.read_epochs_eeglab(), where the presence of channels without position in the .set file caused positions incorrectly assigned to all further channels (#8754 by Mikołaj Magnuski)

• Combining channels of mne.Epochs or mne.Evoked objects now properly retains baseline information (#10703 by Clemens Brunner)

• In mne.Report, some figures would have an undesired border added to the edges; this has now been resolved (#10730 by Richard Höchenberger)

• Fix selection of EEG channels and selected sphere when plotting bridged electrodes with mne.viz.plot_bridged_electrodes() (#10753 by Mathieu Scheltienne)

• Fix broken links in Fixing BEM and head surfaces (#10765 by Alex Rockhill)

• The built-in FieldTrip channel adjacency matrix for easycapM1 had a bug, where the channel PO8 was incorrectly labeled as PO6 This has been resolved by updating the adjacency matrix to the latest version provided by FieldTrip (#10749 by Richard Höchenberger)

• Add a YouTube video tutorial for editing Freesurfer surfaces in Blender to Fixing BEM and head surfaces (#10778 by Alex Rockhill)

• The default interaction style of mne.Evoked.plot_field() has been changed such that if behaves like plot_alignment() when trying to rotate the head (#10788 by Richard Höchenberger)

• Add a video on how to operate the intracranial electrode contact location GUI in Locating intracranial electrode contacts (#10800 by Alex Rockhill)

• Add a video on how to operate the coregistration GUI in Source alignment and coordinate frames (#10802 by Alex Rockhill)

• Add show and block arguments to mne.gui.coregistration() and mne.gui.locate_ieeg() to pop up the GUIs and halt execution of subsequent code respectively (#10802 by Alex Rockhill)

• Correctly report the number of available projections when printing measurement info in a Jupyter notebook (#10471 by Clemens Brunner)

• Fix value set in raw.orig_format for readers of BrainVision (ASCII format), EGI and Artemis123 files (#10851 by Mathieu Scheltienne)

• When reading EGI MFF files, channel names are no longer ignored and reference channel information is properly incorporated (#10898 by Scott Huberty and Daniel McCloy)

• Fix bug in mne.time_frequency.psd_array_welch() and related functions/methods where the bias was not accounted for when average='median' (#10990 by Eric Larson)

• Fix bug in mne.decoding.TemporalFilter where filter parameters were not handled properly (#10968 by Eric Larson)

• Fix documentation bug in ica.plot_sources to specify that picks keyword argument is for picking ICA components to plot (#10936 by Adam Li)

• Annotations contained in EDF files are correctly read as UTF-8 according to the EDF specification (#10963 by Clemens Brunner)

• Fix bug where complex-valued topoplots caused an error, convert to amplitude instead (#10978 by Alex Rockhill)

API and behavior changes

• When creating BEM surfaces via mne.bem.make_watershed_bem() and mne.bem.make_flash_bem(), the copy parameter now defaults to True. This means that instead of creating symbolic links inside the FreeSurfer subject’s bem folder, we now create “actual” files. This should avoid troubles when sharing files across different operating systems and file systems (#10531 by Richard Höchenberger)

• The ordering of channels returned by mne.io.read_raw_nirx() is now ordered by channel name, rather than the order provided by the manufacturer. This enables consistent ordering of channels across different file types (#10555 by Robert Luke)

• For mne.viz.plot_topomap(), mne.viz.plot_evoked_topomap(), mne.viz.plot_arrowmap(), mne.viz.plot_ica_components(), mne.Covariance.plot_topomap(), mne.Evoked.plot_topomap(), mne.Evoked.animate_topomap(), mne.decoding.CSP.plot_patterns(), mne.Projection.plot_topomap() and mne.preprocessing.ICA.plot_components() the topomap image interpolation was previously a cubic interpolation but now can be 'linear' and 'nearest' as well. Unless image_interp='nearest' is passed mne uses a subsequent matplotlib bilinear interpolation to make the interpolated image smoother. Previously, 'image_interp' controlled this second interpolation step and, for the first interpolation, the only option was cubic. To simplify, image_interp is now responsible for the main interpolation and the subsequent matplotlib image interpolation is bilinear but can be changed afterward using im.set_interpolation (#10617 by Alex Rockhill)

• The FLASH BEM surface generation via mne.bem.make_flash_bem() or the mne flash_bem command has now been clarified in terms of expected inputs. In mne.bem.convert_flash_mris() the convert parameter is now deprecated and the flash5 and flash30 now accept list of file names or nibabel images. One breaking change is that now the flash files are looked for as mef05_*.mgz and mef30_*.mgz in mri/flash folder (#10715 by Alex Gramfort)

• plot_compare_evokeds() gets a new parameter time_unit which can be "s" or "ms" (#10950 by Daniel McCloy)

• The to_data_frame methods for Raw, Epochs, Evoked, SourceEstimate, EpochsTFR, and AverageTFR all now have default time_format=None (keep time in seconds) instead of time_format='ms' (convert time to milliseconds) (#10925 by Daniel McCloy)

• mne.Evoked.decimate() now aligns to the sample at time=0 (so that the exact sample when the event occurred is preserved) to be consistent with mne.Epochs.decimate() (#10945 by Alex Rockhill)

Authors

• Adam Li

• Adeline Fecker+

• Alessandro Tonin+

• Alex Ciok+

• Alex Rockhill

• Alexandre Gramfort

• Archit Singhal+

• Ashley Drew+

• Ben Beasley+

• Carina Forster+

• Christian O’Reilly

• Clemens Brunner

• Cora Kim

• Daniel McCloy

• Dominik Welke

• Dominique Makowski

• Eric Larson

• Evan Hathaway

• Frederik D. Weber+

• Guillaume Favelier

• Hamid Maymandi+

• Ilias Machairas+

• Jean-Remi King

• Johann Benerradi

• Jon Houck

• Jona Sassenhagen

• Jordan Drew+

• Lukas Gemein+

• Marijn van Vliet

• Martin Schulz

• Mathieu Scheltienne

• Matt Courtemanche+

• Matthias Dold+

• Matti Toivonen+

• Michiru Kaneda+

• Mikołaj Magnuski

• Mingjian He+

• Naveen Srinivasan+

• Phillip Alday

• Reza Nasri+

• Reza Shoorangiz

• Richard Höchenberger

• Rob Luke

• Scott Huberty+

• Simon Kern

• Sondre Foslien+

• Stefan Appelhoff

• 20. Wang+

• Tziona NessAiver+

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() (:gh:`` 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

Version 0.24.0 (2021-11-03)

Enhancements

• Add pooch to system information reports (#9801 by new contributor Joshua Teves)

• Get annotation descriptions from the name field of SNIRF stimulus groups when reading SNIRF files via mne.io.read_raw_snirf (#9575 by new contributor Darin Erat Sleiter)

• Add support for NIRSport and NIRSport2 devices to mne.io.read_raw_nirx (#9348 and #9401 by new contributor David Julien, new contributor Romain Derollepot, Robert Luke, and Eric Larson)

• New function mne.Dipole.to_volume_labels() to get atlas label for MRI coordinates. (#9376 by new contributor Marian Dovgialo)

• Add support for SURE parameter selection in mne.inverse_sparse.mixed_norm() and make alpha parameter now default to 'sure' (#9430 by new contributor Pierre-Antoine Bannier and Alex Gramfort)

• Speed up BCD solver in mne.inverse_sparse.mixed_norm() by adding Anderson acceleration (#9481 by new contributor Pierre-Antoine Bannier and Alex Gramfort)

• Add support for list of channel types for EEG/sEEG/ECoG/DBS referencing (#9637 by new contributor Mathieu Scheltienne)

• Add the ability to set point size and line width in mne.viz.plot_sensors() and related functions (#9872 by new contributor Dominique Makowski)

• Add support for changing the default event id used by mne.make_fixed_length_epochs() (#9782 by new contributor Mathieu Scheltienne)

• Improve documentation for arguments threshold, method and measure of ICA methods find_bads_ecg, find_bads_ref and find_bads_eog (#9858 by new contributor Mathieu Scheltienne)

• Add support for more than 3 source estimates in mne.viz.plot_sparse_source_estimates() (#9640 by new contributor Pierre-Antoine Bannier and Alex Gramfort)

• Add cortical signal suppression (CSS) mne.preprocessing.cortical_signal_suppression() (#6888, #9892 by new contributor John Samuelsson and Eric Larson)

• Show all good channel types and counts when printing a mne.Info in the notebook (#9725 by Valerii Chirkov and Eric Larson)

• Speed up point decimation in mne.io.read_raw_kit() by vectorization and use of scipy.spatial.cKDTree (#9568 by Jean-Remi King and Eric Larson)

• Add ability to export EDF+ files using mne.export.export_raw() (#9643 by Adam Li)

• New function mne.chpi.get_chpi_info() to retrieve basic information about the cHPI system used when recording MEG data (#9369 by Richard Höchenberger)

• New namespace mne.export created to contain functions (such as mne.export.export_raw and mne.export.export_epochs) for exporting data to non-FIF formats (#9427 by Eric Larson)

• Add support for Hitachi fNIRS devices in mne.io.read_raw_hitachi (#9391 by Eric Larson)

• Add support for picks in mne.stc_near_sensors() (#9396 by Eric Larson)

• Add label methods mne.Label.compute_area and mne.Label.distances_to_outside (#9424 by Eric Larson)

• Add projections when printing a mne.Info in the notebook (#9403 by Alex Gramfort)

• Add new function mne.bem.make_scalp_surfaces() to compute scalp surfaces for coregistration (#9463 by Alex Gramfort)

• Add support for interpolating oxy and deoxyhaemoglobin data types (#9431 by Robert Luke)

• Add support for SNIRF files in mne.Report (#9443 by Robert Luke)

• Add support for exporting MFF evoked files using mne.export.export_evokeds and mne.export.export_evokeds_mff (#9406 by Evan Hathaway)

• mne.concatenate_raws(), mne.concatenate_epochs(), and mne.write_evokeds() gained a new parameter on_mismatch, which controls behavior in case not all of the supplied instances share the same device-to-head transformation (#9438 by Richard Höchenberger)

• Add support for multiple datablocks (acquistions with pauses) in mne.io.read_raw_nihon() (#9437 by Federico Raimondo)

• Add new function mne.preprocessing.annotate_break() to automatically detect and mark “break” periods without any marked experimental events in the continuous data (#9445 by Richard Höchenberger)

• Add “time_format” to mne.io.Raw.plot() and mne.preprocessing.ICA.plot_sources() to display acquisition time on x-axis (#9419 by Martin Schulz)

• Speed up mne.decoding.TimeDelayingRidge.predict() by switching to FFT-based convolution (#9458 by Ross Maddox)

• Show multiple colors and linestyles for excluded components with mne.Evoked in mne.preprocessing.ICA.plot_sources() (#9444 by Martin Schulz)

• Add functions for aligning MRI and CT data mne.transforms.compute_volume_registration and mne.transforms.apply_volume_registration (#9503 by Alex Rockhill and Eric Larson)

• Add tutorial for how to processes image (CT and MR) files in order to localize electrode contacts for intracranial recordings Locating intracranial electrode contacts (#9484 by Alex Rockhill)

• Add vertex number in source space for mne.VolSourceEstimate.plot() and mne.viz.plot_volume_source_estimates() (#9697 by Eric Larson)

• Add support for colormap normalization in mne.viz.plot_topomap() (#9468 by Clemens Brunner)

• Update mne.preprocessing.realign_raw() with Numpy-recommended polynomial fitting method (#9514 by Erica Peterson)

• Add a warning to mne.preprocessing.nirs.beer_lambert_law when source-detector distances are zero (#9541 by Eric Larson)

• Add exclude parameter to mne.io.Raw.plot_psd() and mne.Epochs.plot_psd() (#9519 by Clemens Brunner)

• Add mne.Annotations.rename to rename annotation descriptions (#9525 by Robert Luke)

• Add mne.Annotations.set_durations to set annotation durations (#9529 by Robert Luke)

• The exclude parameter in mne.io.read_raw_edf, mne.io.read_raw_bdf, and mne.io.read_raw_gdf now also accepts a regular expression (#9558 by Clemens Brunner)

• Add mne.Evoked.get_data() method to mne.Evoked (#9555 by Stefan Appelhoff)

• The mne.Epochs.get_data() method now has a units parameter (#9553 by Stefan Appelhoff)

• Add mne.warp_montage_volume to use an anatomical volume with channel locations at high or low insensities to apply a symmetric diffeomorphic registration to a template (e.g. fsaverage) space (#9544 by Alex Rockhill)

• mne.io.Raw.get_data(), mne.Epochs.get_data(), and mne.Evoked.get_data() methods now have tmin and tmax parameters to specify data window in seconds to get (#9556 by Stefan Appelhoff)

• The mne.Evoked.get_data() method now has a units parameter (#9578 by Stefan Appelhoff)

• Add mne.chpi.compute_chpi_snr and mne.viz.plot_chpi_snr for computing and plotting the time-varying SNR of continuously-active HPI coils (#9570 by Daniel McCloy and Jussi Nurminen)

• Add mne.get_montage_volume_labels() to find the regions of interest in a Freesurfer atlas anatomical segmentation for an intracranial electrode montage and mne.viz.plot_channel_labels_circle() to plot them (#9545 by Alex Rockhill)

• Add mne.viz.Brain.add_volume_labels() to plot subcortical surfaces and other regions of interest (#9540 by Alex Rockhill and Eric Larson)

• Add custom cortex curvature colors in mne.viz.Brain via the cortex argument (#9750 by Eric Larson)

• Add mne.channels.DigMontage.apply_trans() to apply a transform directly to a montage (#9601 by Alex Rockhill)

• mne.preprocessing.ICA.fit() now emits a warning if any of the start, stop, reject, and flat parameters are passed when performing ICA on Epochs. These parameters only have an effect on Raw data and were previously silently ignored in the case of Epochs (#9605 by Richard Höchenberger)

• mne.viz.plot_alignment() now emits a warning (instead of aborting with an exception) if the surfaces contain topological defects (#9614 by Richard Höchenberger)

• The coregistration GUI can now display the head surface even if there are topological defects. Previously, a low-resolution standard head unsuitable for individualized coregistration was displayed (#9614 by Richard Höchenberger)

• New mne.coreg.Coregistration object to allow coregistration scripting without a dependency on mayavi (#9516 by Guillaume Favelier).

• Add mne.viz.Brain.add_head() to plot the head surface (#9618 by Alex Rockhill)

• Add mne.channels.read_dig_localite() to read Localite electrode location files (#9658 by Clemens Brunner)

• Add mne.viz.Brain.add_sensors() to plot sensor locations (#9585 by Alex Rockhill)

• Add mne.coreg.estimate_head_mri_t() to estimate the head->mri transform from fsaverage fiducials (#9585 by Alex Rockhill)

• Add mne.channels.DigMontage.add_mni_fiducials() to add fiducials to a montage in MNI coordinates (#9682 by Alex Rockhill)

• Add mne.channels.DigMontage.remove_fiducials() to remove fiducials under rare circumstances when the coordinate frame should not be set to “head” (#9684 by Alex Rockhill)

• Add remove methods for mesh objects in mne.viz.Brain (#9688 by Alex Rockhill)

• Add --show-paths and --developer options to mne sys_info (#9789 by Eric Larson)

• Add ability to export EDF+ files using mne.export.export_raw() (#9643 by Adam Li)

• Reading EDF files via mne.io.read_raw_edf() now can infer channel type from the signal label in the EDF header (#9694 by Adam Li)

• Add mne.gui.locate_ieeg() to locate intracranial electrode contacts from a CT, an MRI (with Freesurfer recon-all) and the channel names from an mne.Info object (#9586 by Alex Rockhill)

• All data fetching code now relies on pooch, which is an added optional requirement for dataset fetchers (#9742 by Adam Li and Daniel McCloy)

• Add phantom FreeSurfer subject fetcher mne.datasets.fetch_phantom() to allow fetching the Otaniemi phantom (#9796 by Eric Larson)

• Add mne.datasets.fetch_dataset() to allow packages to fetch datasets in a similar fashion to MNE (#9763 by Adam Li)

• Add full ECoG dataset to MNE-misc-data and demonstrate its use in How to convert 3D electrode positions to a 2D image and Locating intracranial electrode contacts (#9784 by Alex Rockhill)

• Add options tol and accuracy to mne.fit_dipole() to control optimization (#9810 by Eric Larson)

• Completely revamp the Report experience: new HTML layout, many new methods, more flexibility; the functionality is demonstrated in Getting started with mne.Report (#9754, #9828, #9847, #9860, #9861, #9862, #9863, #9871, #9881, #9891, #9901 by Richard Höchenberger, Eric Larson, and Alex Gramfort)

• Add basic HTML representations of Forward and InverseOperator instances for a nicer Jupyter experience (#9754 by Richard Höchenberger)

• mne.io.read_raw_brainvision now handles ASCII data with comma-separated values, as may be exported from BrainVision Analyzer (#9795 by Richard Höchenberger)

• Add mne.preprocessing.ieeg.project_sensors_onto_brain() to project ECoG sensors onto the pial surface to compensate for brain shift (#9800 by Alex Rockhill)

• Add support for data acquired with NIRx devices using Aurora software version 2021.9 (#9800 by Robert Luke, and Eric Larson)

• All functions for reading and writing files should now automatically handle ~ (the tilde character) and expand it to the user’s home directory. Should you come across any function that doesn’t do it, please do let us know! (#9613, #9845 by Richard Höchenberger)

• All functions accepting a FreeSurfer subjects directory via a subjects_dir parameter can now consume pathlib.Path objects too (used to be only strings) (#9613 by Richard Höchenberger)

• Add support for colormap normalization in mne.time_frequency.AverageTFR.plot() (#9851 by Clemens Brunner)

• Add support for BIDS-compatible filenames when splitting big epochs files via the new split_naming parameter in mne.Epochs.save() (#9869 by Denis Engemann)

• Add by_event_type parameter to mne.Epochs.average() to create a list containing an mne.Evoked object for each event type (#9859 by Marijn van Vliet)

• Add pyqtgraph as a new backend for mne.io.Raw.plot() (#9687 by Martin Schulz)

• Add mne.viz.set_browser_backend(), mne.viz.use_browser_backend() and mne.viz.get_browser_backend() to set matplotlib or pyqtgraph as backend for mne.io.Raw.plot() (#9687 by Martin Schulz)

Bugs

• Fix bug in mne.io.Raw.pick() and related functions when parameter list contains channels which are not in info instance (#9708 by new contributor Evgeny Goldstein)

• Fix a few typos (#9706 by new contributor Timothy Gates)

• Fix bug with mne.Epochs.crop() and mne.Evoked.crop() when include_tmax=False, where the last sample was always cut off, even when tmax > epo.times[-1] (#9378 by new contributor Jan Sosulski)

• Fix bug with mne.io.read_raw_curry to allow reading Curry 7 and 8 event files with ‘.ceo’ and ‘.cdt.ceo’ extensions (#9381, #9712 by new contributor Xiaokai Xia, Daniel McCloy, and by new contributor Reza Shoorangiz)

• Fix bug with mne.compute_rank, mne.cov.compute_whitener and mne.preprocessing.ICA.fit when explicit picks including bad channels are provided (#9719 by new contributor Mathieu Scheltienne)

• Fix bug with mne.concatenate_epochs() where the concatenated events could end up in non-chronological order. (#9765 by new contributor Jan Sosulski)

• Fix bug where mne.time_frequency.psd_array_welch() and mne.time_frequency.psd_array_multitaper() failed to handle negative integer for n_jobs argument (#9849 by new contributor Riessarius Stargardsky)

• Fix bug where resampling returns empty instances (#9897 by new contributor Mathieu Scheltienne and Eric Larson)

• Fix bug with mne.io.Raw.get_montage now returning both good and bad channels in the montage. (#9920 by new contributor Mathieu Scheltienne)

• Fix bug with mne.io.read_raw_nihon() where latin-1 annotations could not be read (#9384 by Alex Gramfort)

• Fix bug when printing a mne.io.RawArray in the notebook (#9404 by Alex Gramfort)

• Fix bug when computing rank from info for SSS data with only gradiometers or magnetometers (#9435 by Alex Gramfort)

• Fix bug with mne.preprocessing.find_bad_channels_maxwell where all-flat segments could lead to an error (#9531 by Eric Larson)

• Fix bug with mne.io.Raw.set_montage and related functions where the channel coordinate frame was not properly set to head (#9447 by Eric Larson)

• Fix bug with mne.io.read_raw_fieldtrip and mne.read_epochs_fieldtrip where channel positions were not set properly (#9447 by Eric Larson)

• Fix bug with mne.io.read_raw_kit() where omitting HPI coils could lead to an AssertionError on reading (#9612 by Eric Larson)

• Fix bug with mne.io.read_raw_edf() where reading only stimulus channels would lead to an error (#9831 by Eric Larson)

• Fix bug with mne.preprocessing.nirs.optical_density where protection against zero values was not guaranteed (#9522 by Eric Larson)

• mne.concatenate_raws() now raises an exception if raw.info['dev_head_t'] differs between files. This behavior can be controlled using the new on_mismatch parameter (#9438 by Richard Höchenberger)

• Fixed bug in mne.Epochs.drop_bad() where subsequent rejections failed if they only specified thresholds for a subset of the channel types used in a previous rejection (#9485 by Richard Höchenberger).

• Fix bug with mne.simulation.simulate_evoked, mne.apply_forward, and mne.apply_forward_raw where systems with EEG channels that come before MEG channels would have them mixed up in the output evoked or raw object (##9513 by Eric Larson)

• In mne.viz.plot_ica_scores() and mne.preprocessing.ICA.plot_scores(), the figure and axis titles no longer overlap when plotting only a single EOG or ECG channel (#9489 by Richard Höchenberger).

• Ensure mne.io.Raw.get_montage works with SNIRF data (#9524 by Robert Luke)

• Fix bug in mne.setup_volume_source_space() where non-finite positions could be used in a discrete source space (#9603 by Eric Larson)

• Fix bug in mne.viz.plot_topomap() (and related methods like mne.Evoked.plot_topomap()) where large distances between electrodes (higher than head radius) would lead to an error (#9528 by Mikołaj Magnuski).

• Fix bug in mne.viz.plot_topomap (and related methods) where passing axes that are part of a matplotlib figure that uses a constrained layout would emit warnings (#9558 by Eric Larson)

• Fix bug in mne.make_forward_solution() where impossible sensor-BEM geometries were not checked (#9893 by Eric Larson)

• Fix bug in mne.concatenate_epochs() when concatenating mne.Epochs objects with 0 events (#9535 by Marijn van Vliet)

• Fix bug in mne.viz.Brain.screenshot() where the RGBA mode was not supported (#9564 by Guillaume Favelier).

• Fix bug in mne.io.read_raw_egi() where reading data from a data segment that is part of an acquisition skip would lead to an error (#9565 by Eric Larson)

• Prevent mne.io.Raw.plot() windows from spawning at sizes too small to properly render (#9629 by Daniel McCloy)

• Fix bug where mne.io.Raw.plot() raised an error when plotting raw dipole data (#9771 by Eric Larson)

• Fix bug in :mne.preprocessing.ICA.find_bads_ecg() where passing start and stop lead to erroneous data windows depending on the combination of Raw, Epochs, Evoked, and the type (int, float, None) of start and stop (#9556 by Stefan Appelhoff)

• Fix bug in mne.viz.set_3d_backend() and mne.viz.get_3d_backend() where the PyVistaQt-based backend was ambiguously named 'pyvista' instead of 'pyvistaqt'; use set_3d_backend('pyvistaqt') and expect 'pyvistaqt' as the output of mne.viz.get_3d_backend() instead of 'pyvista', and consider using get_3d_backend().startswith('pyvista') for example for backward-compatible conditionals (#9607 by Guillaume Favelier)

• Fix bug in mne.viz.plot_compare_evokeds() where confidence bands were not drawn if only one condition was plotted (#9663 by Daniel McCloy)

• Fix bug where setting of a montage with fNIRS data got set to “unknown” coordinate frame when it should have been in “head” (#9630 by Alex Rockhill)

• Fix bug where “seeg”, “ecog”, “dbs” and “fnirs” data had coordinate frame unknown upon loading from a file when it should have been in “head” (#9580 by Alex Rockhill)

• Raise error when no trans is provided to mne.viz.plot_alignment() when required instead of assuming identity head->mri transform (#9585 by Alex Rockhill)

• Fix bug where mne.Epochs.equalize_event_counts() failed when only one good epoch existed for one of the event types (#9758 by Daniel McCloy)

• Fix bug where channels with a dollar sign ($) were not being labeled “misc” in mne.io.read_raw_nihon() (#9695 by Adam Li)

• Fix bug where mne.io.read_raw_persyst() was lower-casing events it found in the .lay file (#9746 by Adam Li)

• Fix bug with Qhull when plotting OPM sensors in mne.viz.plot_alignment() (#9799 and #9804 by Eric Larson)

• Fix bug where mne.io.read_raw_snirf() was including the landmark index as a spatial coordinate (#9777 by Robert luke)

• Fix bug where mne.Annotations were not appending channel names when being added together (#9780 by Adam Li)

• mne.viz.plot_evoked_joint now correctly handles a times='peaks' parameter value (#9754 by Richard Höchenberger)

• In mne.viz.plot_compare_evokeds, slightly adjust the x-axis limit calculation to avoid drawing an axis that is too short (#9754 by Richard Höchenberger)

• Fix a bug with mne.viz.snapshot_brain_montage() with the Mayavi backend where electrodes were shown in the wrong positions, and with the PyVista backend where the snapshot always contained the electrodes but could be missing a hemisphere (#9933 by Eric Larson)

• In mne.io.Raw.plot_psd() and mne.Epochs.plot_psd(), avoid overlap between subplot titles and x-axis tick labels (#9864 by Richard Höchenberger)

• In mne.Epochs.plot_psd_topomap(), the data is now scaled to match the output of mne.Epochs.plot_psd() (#9873 by Richard Höchenberger)

• Fix channel locations with NaN values causing all channel locations not to be plotted in mne.viz.Brain.add_sensors() (#9911 by Alex Rockhill)

• Fix infinite loop bug in mne.get_montage_volume_labels() (#9940 by Alex Rockhill)

API changes

• The mne.Info class is now more strictly checked when attributes are set. Setting most attributes directly will lead to an error in the next release. See the docstring of mne.Info for more information (#9867 by new contributor Mathieu Scheltienne)

• The Mayavi 3D backend has been deprecated (#9904 by Eric Larson):

  • In 3D plotting functions, use PyVista-based backends ('pyvistaqt' and 'notebook') as PySurfer/Mayavi will be removed in the next version

  • To use the mne kit2fiff command-line GUI for fiducial markers, install the separate mne-kit-gui module, which can still be launched via $ mne kit2fiff

  • The mne.gui.fiducials GUI has been deprecated, use mne coreg or mne_kit_gui.fiducials() to set MRI fiducials instead

• In mne.compute_source_morph, the niter_affine and niter_sdr parameters have been replaced by niter and pipeline parameters for more consistent and finer-grained control of registration/warping steps and iteration (#9505 by Alex Rockhill and Eric Larson)

• Split mne.viz.Brain.show_view() argument view into azimuth, elevation and focalpoint for clearer view setting and make the default for row and col apply to all rows and columns (#9596 by Alex Rockhill)

• Deprecate solver='prox' in mne.inverse_sparse.mixed_norm() in favor of solver='cd' and solver='bcd' as coordinate descent solvers consistently outperform proximal gradient descent (#9608 by Pierre-Antoine Bannier)

• All mne.connectivity functions have moved to the mne-connectivity package; they are deprecated in MNE-Python and will be removed in version 0.25 (#9493 by Adam Li).

• mne.inverse_sparse.mixed_norm() now simply warns when source estimates contain no dipole, e.g. if data are too noisy and alpha is based on SURE (#9685 by Alex Gramfort)

• Deprecate functions mne.datasets.DATASET_NAME.has_DATASET_NAME_data() for these datasets: epilepsy_ecog, fnirs_motor, multimodal, opm, phantom_4dbti, refmeg_noise, sample, somato, and ssvep. Use the generic mne.datasets.has_dataset() instead (#9781 by Daniel McCloy and Adam Li)

• mne.Report modernization has led to multiple deprecations (#9754 by Richard Höchenberger):

  • mne.Report.add_figs_to_section and mne.Report.add_slider_to_section have been deprecated in favor of mne.Report.add_figure()

  • mne.Report.add_images_to_section has been deprecated in favor of mne.Report.add_image()

  • mne.Report.add_bem_to_section has been deprecated in favor of mne.Report.add_bem()

  • mne.Report.add_htmls_to_section has been deprecated in favor of mne.Report.add_html()

  • In mne.Report.parse_folder(), the sort_sections parameter has been deprecated in favor of sort_content

  • In mne.Report.remove(), the caption and section parameters have been deprecated in favor of title and tags, respectively

  • The mne.Report.sections attribute has been deprecated in favor of mne.Report.tags

  • The mne.Report.fnames attribute has been deprecated without replacement

• mne.Epochs.plot() and mne.viz.plot_epochs() gained parameter show_scalebars analogous to mne.viz.plot_raw() (#9815 by Daniel McCloy)

• The output folder name for HF_SEF datasets is now hf_sef instead of HF_SEF (#9763 by Adam Li)

• Deprecate mne.viz.utils.center_cmap (#9851 by Clemens Brunner)

• The default partial pathlength factor of mne.preprocessing.nirs.beer_lambert_law() will change from 0.1 in 0.24 to 6.0 in the next release (#9843 by Robert Luke)

• mne.preprocessing.ICA.detect_artifacts has been deprecated. Please use find_bads_eog and find_bads_ecg instead (#9909 by Richard Höchenberger)

Authors

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

• Adam Li

• Alex Rockhill

• Alexandre Gramfort

• Britta Westner

• Clemens Brunner

• Daniel McCloy

• Darin Erat Sleiter+

• David Julien+

• Denis A. Engemann

• Dominique Makowski+

• Eric Larson

• Erica Peterson

• Evan Hathaway

• Evgeny Goldstein+

• Fede Raimondo

• Gansheng Tan+

• Guillaume Favelier

• Hubert Banville

• Jan Sosulski+

• Jean-Remi King

• Jeff Stout

• Johann Benerradi

• John Samuelsson+

• Josh Koen+

• Joshua Teves+

• Lukas Hecker+

• Luke Bloy

• Marian Dovgialo+

• Marijn van Vliet

• Martin Schulz

• Mathieu Scheltienne+

• Mikołaj Magnuski

• Pierre-Antoine Bannier+

• Reza Shoorangiz+

• Richard Höchenberger

• Riessarius Stargardsky+

• Robert Luke

• Romain Derollepot+

• Ross Maddox

• Ryan Law+

• Stefan Appelhoff

• Steve Matindi+

• Timothy Gates+

• Valerii Chirkov

• Xiaokai Xia+

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 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-Remi 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-Remi 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+

Version 0.22.0 (2020-12-17)

Enhancements

• Add mne.read_evokeds_mff() to read averaged MFFs (requires mffpy >= 0.5.7) by new contributor Evan Hathaway (#8354)

• Add mne.decoding.SSD for spatial filtering with spatio-spectral-decomposition (#7070 by new contributor Victoria Peterson and Denis Engemann)

• Add reader for optical imaging data recorded using ISS Imgagent I/II hardware and BOXY recording software in mne.io.read_raw_boxy() (#7717 by new contributor Jonathan Kuziek and Kyle Mathewson)

• Add options to use labels in mne.minimum_norm.get_point_spread() and mne.minimum_norm.get_cross_talk() (#8275 by Olaf Hauk)

• Update surfaces argument in mne.viz.plot_alignment() to allow dict for transparency values, and set default for sEEG data to have transparency (#8445 by Keith Doelling)

• Add support for mri_fiducials='estimated' in mne.viz.plot_alignment() to allow estimating MRI fiducial locations using mne.coreg.get_mni_fiducials() (#8553 by Eric Larson)

• Update default values in mne coreg and mne.viz.plot_alignment() for clearer representation of MRI and digitized fiducial points (#8553 by Alex Gramfort and Eric Larson)

• Add n_pca_components argument to mne.viz.plot_ica_overlay() (#8351 by Eric Larson)

• Add mne.stc_near_sensors() to facilitate plotting ECoG data (#8190 by Eric Larson)

• Add proj argument to mne.make_fixed_length_epochs() (#8351 by Eric Larson)

• Add mne.preprocessing.realign_raw() to realign simultaneous raw recordings in the presence of clock drift (#8539 by Eric Larson)

• Reduce memory usage of volume source spaces (#8379 by Eric Larson)

• Speed up heavy use of mne.SourceMorph.apply() for volumetric source spaces by use of the method mne.SourceMorph.compute_vol_morph_mat() (#8366 by Eric Larson)

• Add support for non-uniform zooms (e.g., when using a surrogate MRI via mne.scale_mri()) in volumetric morphing (#8642 by Eric Larson)

• In mne.compute_source_morph() zooms are no longer required to match the spacing of src_to, which is useful to ensure the morphing is accurate when the src_to spacing is large (e.g., 1 cm) (#8642 by Eric Larson)

• Add volumetric source space support to mne.labels_to_stc() (#8447 by Eric Larson)

• Speed up mne.decoding.TimeDelayingRidge with edge correction using Numba (#8323 by Eric Larson)

• Add mne.Epochs.reset_drop_log_selection() to facilitate writing epochs with many ignored entries in their drop log (#8449 by Eric Larson)

• Add sEEG source visualization using mne.stc_near_sensors() and sEEG working tutorial (#8402 by Eric Larson and Adam Li)

• Add mne.channels.DigMontage.get_positions(), which will return a dictionary of channel positions, coordinate frame and fiducial locations (#8460 by Adam Li)

• Add support for writing digitization points in a coordinate frame other than head in mne.channels.DigMontage.save() (#8532 by Eric Larson)

• Add picks parameter to mne.preprocessing.fix_stim_artifact() to specify which channel needs to be fixed (#8482 by Alex Gramfort)

• Add progress bar support to mne.time_frequency.csd_morlet() (#8608 by Eric Larson)

• Further improved documentation building instructions and execution on Windows (#8502 by kalenkovich and Eric Larson)

• Add option to disable TQDM entirely with MNE_TQDM='off' (#8515 by Eric Larson)

• Add option on_header_missing to mne.channels.read_polhemus_fastscan() (#8622 by Eric Larson)

• Add option window to mne.time_frequency.psd_welch and related functions (#8862 by Eric Larson)

• mne.preprocessing.ICA.plot_sources now displays an mne.preprocessing.ICA.plot_properties window when right-clicking on component names on the y-axis (#8381 by Daniel McCloy)

• mne.io.read_raw_edf(), mne.io.read_raw_bdf(), and mne.io.read_raw_gdf() now detect and handle invalid highpass/lowpass filter settings (#8584 by Clemens Brunner)

• If a baseline tuple containing one or two None values – e.g. (None, 0), (0, None), or (None, None) – is passed to Epochs or apply_baseline, the None value(s) will be replaced with the actual time (i.e., tmin and tmax, respectively) when populating Epochs.baseline (#8442 by Richard Höchenberger)

• Epochs will now retain the information about an applied baseline correction, even if the baseline period is partially or completely removed through cropping later on (#8442 by Richard Höchenberger)

• Add mne.source_space.compute_distance_to_sensors() to compute distances between vertices and sensors (#8534 by Olaf Hauk and Marijn van Vliet)

• Annotations can now be shown/hidden interactively in raw plots (#8624 by Daniel McCloy)

• Added argument colors to mne.grow_labels (#8519 by Olaf Hauk)

• Added mne.SourceEstimate.apply_baseline method for baseline-correction of source estimates (#8452 by Olaf Hauk)

• New mne.viz.Brain.set_time method to set the displayed time in seconds (#8415 by Daniel McCloy)

• Update the backend parameter of mne.viz.plot_source_estimates() to integrate pyvista (#8395 by Guillaume Favelier)

• Add group_by parameter to mne.viz.plot_epochs and mne.Epochs.plot to allow displaying channel data by sensor position (#8381 by Daniel McCloy)

Bugs

• Fix orthogonalization of power envelopes in mne.connectivity.envelope_correlation (#8658 by new contributor Qianliang Li and Eric Larson)

• Fix data overwrite of cascading simulation operations :mne.simulation.simulate_raw (#8633 by new contributor Jeff Stout)

• Fix a transpose issue of mne.decoding.CSP.plot_filters() (#8580 by new contributor Hongjiang Ye)

• Fix mne.io.read_raw_curry() to deal with Curry datasets that have channels that are listed in the labels file, but which are absent from the saved data file (e.g. ‘Ref’ channel). Also now populates info[‘meas_date’] if possible (#8400 by new contributor Tod Flak)

• Fix bug with mne.io.egi.tests/test_egi.py where it mandatorily downloaded testing data when it was not necessary (#8474 by new contributor Aniket Pradhan)

• Fix bug with reading split files that have dashes in the filename (#8339 by new contributor Eduard Ort)

• Fix bug with parsing EDF dates and date integers (#8558 by new contributor Austin Hurst and Eric Larson)

• Fix bug with reading EDF and KIT files on big endian architectures such as s390x (#8618 by Eric Larson)

• Fix bug with mne.beamformer.make_dics() where the rank parameter was not properly handled (#8594 by Marijn van Vliet and Eric Larson)

• Fix bug with mne.beamformer.apply_dics() where the whitener was not properly applied (#8610 by Eric Larson)

• Fix bug with plot_epochs_image when order is supplied and multiple conditions are plotted (#8377 by Daniel McCloy )

• Fix bug with mne.viz.plot_source_estimates() when using the PyVista backend where singleton time points were not handled properly (#8285 by Eric Larson)

• Fix bug when passing axes to plotting functions, matplotlib.pyplot.tight_layout() will not be called when the figure was created using a constrained layout (#8344 by Eric Larson)

• Fix bug with compensated CTF data when picking channels without preload (#8318 by Eric Larson)

• Fix bug with plotting MEG topographies where the wrong extrapolation made was used in ICA (#8637 by Eric Larson)

• Fix bug when merging fNIRS channels in mne.viz.plot_evoked_topomap() and related functions (#8306 by Robert Luke)

• Fix bug where events could overflow when writing to FIF (#8448 by Eric Larson)

• mne.io.read_raw_edf() now supports EDF files with invalid recording dates (#8283 by Clemens Brunner)

• Fix bug with mne.io.Raw.save() when using split_naming='bids' where non-split files would still be named name_split-01_meg.fif instead of the requested name_meg.fif (#8464 by Alex Gramfort and Eric Larson)

• Fix bug with mne.preprocessing.ICA where n_pca_components as a float would give the number of components that explained less than or equal to the given variance. It now gives greater than the given number for better usability and consistency with sklearn.decomposition.PCA. Generally this will mean that one more component will be included (#8326 by Eric Larson)

• Fix bug with mne.preprocessing.ICA where projections were not tracked properly (#8343 by Eric Larson)

• Fix bug where extrapolation points created artifacts in mne.viz.plot_evoked_topomap() and related functions (#8425 by Mikołaj Magnuski)

• Fix bug with mne.preprocessing.read_ica_eeglab() where full-rank data were not handled properly (#8326 by Eric Larson)

• Fix bug with Somatosensory where the BEM was not included (#8317 by Eric Larson)

• Fix bug with coordinate frames when performing volumetric morphs via mne.compute_source_morph() and mne.SourceMorph.apply() that could lead to ~5 mm bias (#8642 by Eric Larson)

• Fix bug with volumetric rendering alpha in mne.VolSourceEstimate.plot_3d() and related functions (#8663 by Eric Larson)

• Fix missing documentation of mne.io.read_raw_nihon() in Importing data from EEG devices (#8320 by Adam Li)

• Fix bug with mne.add_reference_channels() when mne.io.Raw.reorder_channels() or related methods are used afterward (#8303, ##8484 by Eric Larson)

• Fix bug where the verbose arguments to mne.Evoked.apply_baseline() and mne.Epochs.apply_baseline() were not keyword-only (#8349 by Eric Larson)

• ICA.max_pca_components will not be altered by calling fit anymore. Instead, the new attribute ICA.max_pca_components_ will be set (#8321 by Richard Höchenberger)

• Fix bug that plot_ica_overlay would sometimes not create red traces (#8341 by Richard Höchenberger)

• Fix bug with ICA where n_components=None, n_pca_components=None could lead to unstable unmixing matrix inversion by making n_components=None also use the lesser of n_components=0.999999 and n_components=n_pca_components (#8351 by Eric Larson)

• The ica.n_pca_components property is no longer be updated during mne.preprocessing.ICA.fit(), instead ica.n_components_ will be added to the instance (#8351 by Eric Larson)

• Pass rank everyhwere in forward preparation for source imaging. This bug affected sparse solvers when using maxfilter data (#8368 by Alex Gramfort)

• Fix bug in mne.viz.plot_alignment() where ECoG and sEEG channels were not plotted and fNIRS channels were always plotted in the head coordinate frame (#8393 by Eric Larson)

• Fix bug in mne.set_bipolar_reference() where ch_info could contain invalid channel information keys (#8416 by Eric Larson)

• When reading BrainVision raw data, the channel units and types were sometimes not inferred correctly (#8434 by Richard Höchenberger)

• Attempting to remove baseline correction from preloaded Epochs will now raise an exception (#8435 by Richard Höchenberger)

• mne.Report.parse_folder() will now correctly handle split FIFF files (#8486, #8491 by Richard Höchenberger)

• Fix bug where BrainVision channel names, event types, and event descriptions containing commas were incorrectly parsed (#8492 by Stefan Appelhoff)

• Fix bug in mne.preprocessing.compute_fine_calibration() where the magnetometer calibration coefficients were computed incorrectly (#8522 by Eric Larson)

• Fix bug in mne.io.read_raw_eeglab() where empty event durations led to an error (#8384 by Mikołaj Magnuski)

• Fix inset sensor plots to always use equal aspect (#8545 by Daniel McCloy)

• Fix bug in mne.viz.plot_compare_evokeds where evokeds with identical comment attributes would not plot properly if passed as a list (#8590 by Daniel McCloy)

• Fix bug in mne.time_frequency.psd_welch and related functions where the window default errantly changed from 'hamming' to ('tukey', 0.25) (#8862 by Eric Larson)

• Fix bug in mne.io.read_raw_kit() where scale factors for EEG channels could be set to zero (#8542 by Eric Larson)

• Fix reading GDF files with excluded channels in mne.io.read_raw_gdf() (#8520 by Clemens Brunner)

• Fix automatic selection of extrapolation mask type from channel type when plotting field maps (#8589 by Daniel McCloy)

• Fix bug in mne.viz.set_3d_title() where 3D plot could have multiple titles that overlap (#8564 by Guillaume Favelier)

• Fix bug in mne.viz.set_3d_view() where plotter is not updated properly causing camera issues in the doc (#8564 by Guillaume Favelier)

• mne.preprocessing.find_ecg_events() didn’t take the tstart parameter value into account when calculating the average heart rate (#8605 by Richard Höchenberger)

API changes

• Minimum required versions were increased for core dependencies NumPy (1.15.4), SciPy (1.1.0), and Matplotlib (3.0) and for the optional dependencies scikit-learn (0.20.2) and pandas (0.23.4) (#8374 by Eric Larson)

• The parameter on_split_missing has been added to mne.io.read_raw_fif() and its default will change from 'warn' to 'raise' in 0.23, by (#8357 Eric Larson)

• The max_pca_components argument of ICA has been deprecated, use n_components during initialization and n_pca_components in apply() instead (#8351 by Eric Larson)

• The n_pca_components argument of ICA has been deprecated, use n_pca_components in apply() (#8356 by Eric Larson)

• The trans argument of mne.extract_label_time_course() is deprecated and will be removed in 0.23 as it is no longer necessary (#8389 by Eric Larson)

• Parameter event_colors in mne.viz.plot_epochs and mne.Epochs.plot is deprecated, replaced by event_color which is consistent with mne.viz.plot_raw and provides greater flexibility (#8381 by Daniel McCloy)

Authors

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

• Adam Li

• Alexandre Gramfort

• Aniket Pradhan +

• Austin Hurst +

• Christian Brodbeck

• Clemens Brunner

• Daniel McCloy

• Denis A. Engemann

• Eduard Ort +

• Eric Larson

• Evan Hathaway +

• Evgenii Kalenkovich

• Fede Raimondo

• Guillaume Favelier

• Hongjiang Ye +

• Jean-Remi King

• Jeff Stout +

• Jonathan Kuziek +

• Jussi Nurminen

• Justus Schwabedal

• Keith Doelling

• Kyle Mathewson

• Mads Jensen

• Mainak Jas

• Marijn van Vliet

• Mikolaj Magnuski

• Olaf Hauk

• Qianliang Li +

• Richard Höchenberger

• Robert Luke

• Stefan Appelhoff

• Thomas Hartmann

• Tod Flak +

• Victoria Peterson +

Version 0.21 (2020-09-21)

Enhancements

• Modified mne.Epochs.pick_types() to remove dropped channel types from reject and flat dictionaries by new contributor Rahul Nadkarni

• Add function mne.preprocessing.regress_artifact() to remove artifacts using linear regression by new contributor Kyle Mathewson and Eric Larson

• Add sources and detectors options for fNIRS use of mne.viz.plot_alignment() allowing plotting of optode locations in addition to channel midpoint channels and path between fNIRS optodes by new contributor Kyle Mathewson

• BrainVision data format files are now parsed for EEG impedance values in mne.io.read_raw_brainvision() and provided as a .impedances attribute of raw by new contributor Jan Sedivy and Stefan Appelhoff

• Add function mne.channels.combine_channels() to combine channels from Raw, Epochs, or Evoked according to ROIs (combinations including mean, median, or standard deviation; can also use a callable) by new contributor Johann Benerradi

• Improved documentation building instructions and execution on Windows by new contributor Martin Schulz, kalenkovich, and Eric Larson

• Speed up reading of annotations in EDF+ files by new contributor Jeroen Van Der Donckt

• Add head to mri and mri to voxel space transform details to Source alignment and coordinate frames tutorial, by Alex Rockhill

• Improve memory efficiency of mne.concatenate_epochs() by Eric Larson

• Allow picking channels in raw instances (e.g., mne.io.Raw.pick_types()) without preloading data, by Eric Larson

• mne.preprocessing.ICA.plot_sources() now plots annotation markers similar to mne.io.Raw.plot() by Luke Bloy

• Add support for scalar multiplication and division of mne.time_frequency.AverageTFR instances by Luke Bloy

• Add support for signals in mV for mne.io.read_raw_brainvision() by Clemens Brunner

• mne.Epochs.plot_psd_topomap() and mne.viz.plot_epochs_psd_topomap() now allow joint colorbar limits across subplots, by Daniel McCloy.

• Add support for using loose-orientation surface priors with free-orientation volume priors in mixed source space inverses by Eric Larson

• Add mne.MixedVectorSourceEstimate for vector source estimates for mixed source spaces, by Eric Larson

• Add mixed and volumetric source estimate plotting using volumetric ray-casting to mne.MixedSourceEstimate.plot() and mne.VolSourceEstimate.plot_3d() by Eric Larson

• Add mne.MixedSourceEstimate.surface() and mne.MixedSourceEstimate.volume() methods to allow surface and volume extraction by Eric Larson

• Add mne.VectorSourceEstimate.project() to project vector source estimates onto the direction of maximum source power by Eric Larson

• Add support to mne.extract_label_time_course() for vector-valued and volumetric source estimates by Eric Larson

• Add method mne.VolSourceEstimate.in_label() by Eric Larson

• Add support for mixed source spaces to mne.compute_source_morph() by Eric Larson

• Add support for volume and mixed source spaces to mne.stats.summarize_clusters_stc() by Eric Larson

• Add support for omitting the SDR step in volumetric morphing by passing n_iter_sdr=() to mne.compute_source_morph by Eric Larson

• Add single_volume argument to mne.setup_volume_source_space() to facilitate creating source spaces with many volumes (e.g., all subvolumes of aseg.mgz) by Eric Larson

• Add support for passing a string argument to bg_img in mne.viz.plot_volume_source_estimates by Eric Larson

• Add support for providing the destination surface source space in the src_to argument of mne.compute_source_morph() by Eric Larson

• Add explained variance logging to mne.inverse_sparse.mixed_norm(), mne.inverse_sparse.gamma_map(), and mne.beamformer.rap_music() by Eric Larson

• Add tol_kind option to mne.compute_rank() by Eric Larson

• Allow resampling raw data with mne.io.Raw.resample() without preloading data, by Eric Larson

• Allow using pick_ori='vector' with a fixed-orientation inverse to facilitate visualization with mne.viz.plot_vector_source_estimates() by Eric Larson

• mne.viz.plot_dipole_locations() and mne.Dipole.plot_locations() gained a title argument to specify a custom figure title in orthoview mode by Richard Höchenberger

• Add orientations projected onto the MRI slices in mne.viz.plot_dipole_locations() in 'orthoview' mode by Eric Larson

• Add temporal derivative distribution repair (TDDR) mne.preprocessing.nirs.temporal_derivative_distribution_repair() with shortened alias mne.preprocessing.nirs.tddr by Robert Luke

• Add mne.read_freesurfer_lut() to make it easier to work with volume atlases by Eric Larson

• Add support for overlap-add processing when method='spectrum_fit' in mne.io.Raw.notch_filter() by Eric Larson

• Add functionality to interpolate bad NIRS channels by Robert Luke

• Add ability to interpolate EEG channels using minimum-norm projection in mne.io.Raw.interpolate_bads() and related functions with method=dict(eeg='MNE') by Eric Larson

• Added ability of mne.io.read_raw_nirx() to open data by passing path to header file Robert Luke

• Add mne.channels.DigMontage.rename_channels() to allow renaming montage channels by Eric Larson

• Document mne.channels.compute_native_head_t() to allow computing the native-to-head transformation that will be applied when doing raw.set_montage and related functions by Eric Larson

• Add support to in mne.io.Raw.plot() for passing clipping as a float to clip to a proportion of the dedicated channel range by Eric Larson

• Add function mne.preprocessing.annotate_muscle_zscore() to annotate periods with muscle artifacts. by Adonay Nunes

• Add mne.stats.ttest_ind_no_p() to mirror mne.stats.ttest_1samp_no_p() with hat correction by Eric Larson

• Add mne.stats.combine_adjacency to combine adjacency matrices for independent data dimensions to enable things like spatio-temporal-time-frequency clustering in mne.stats.permutation_cluster_test by Eric Larson

• Speed up raw data reading without preload in mne.io.read_raw_nirx() by Eric Larson

• Speed up mne.Epochs.copy() and mne.Epochs.__getitem__() by avoiding copying immutable attributes by Eric Larson

• Speed up and reduce memory usage of mne.SourceEstimate.plot() and related functions/methods when show_traces=True by Eric Larson

• Reduce memory usage of plot_psd, mne.time_frequency.psd_welch, and psd_array_welch for long segments of data by Eric Larson

• Support for saving movies of source time courses (STCs) with brain.save_movie method and from graphical user interface by Guillaume Favelier

• Add mri and show_orientation arguments to mne.viz.plot_bem() by Eric Larson

• Add mne.viz.centers_to_edges() to help when using matplotlib.axes.Axes.pcolormesh() with flat shading by Eric Larson

• Add on_missing='raise' to mne.io.Raw.set_montage() and related functions to allow ignoring of missing electrode coordinates by Adam Li

• Add on_missing='raise' to mne.viz.plot_events() to allow ignoring missing events when passing event_id by Eric Larson

• Add REST EEG infinity reference scheme to mne.io.Raw.set_eeg_reference() and related functions by Eric Larson

• Add better sanity checking of max_pca_components and n_components to provide more informative error messages for mne.preprocessing.ICA by Eric Larson

• Add plot option to mne.viz.plot_filter() allowing selection of which filter properties are plotted and added option for user to supply axes by Robert Luke

• Add estimation method legend to mne.viz.plot_snr_estimate() by Eric Larson

• Add support to mne.SourceSpaces.export_volume for mri_resolution='sparse' to color only the nearest-neighbor voxels instead of entire regions by Eric Larson

• Add axes argument to mne.viz.plot_evoked_white(), mne.Evoked.plot_white(), and mne.viz.plot_snr_estimate() by Eric Larson

• Change default to surfaces='auto' from surfaces='head' to allow mne.viz.plot_alignment() to work when just passing a mne.Info as plot_alignment(info) by Eric Larson

• Add ECoG misc EDF dataset to the Working with ECoG data tutorial to show snapshots of time-frequency activity by Adam Li

• Add mne.viz.set_3d_options() and MNE_3D_OPTION_ANTIALIAS environment variable to control full-scene antialiasing (FXAA) in 3D functions like mne coreg, mne.viz.plot_alignment(), and mne.viz.plot_source_estimates(); this can be useful on systems where FXAA does not work well, such as some with MESA software rendering, by Eric Larson

• Add config variable MNE_TQDM to support explicitly setting the TQDM backend to use, for example tqdm or tqdm.auto (default) by Eric Larson

• Add better support for reading corrupted FIF files in mne.io.read_raw_fif() by Eric Larson

• BIDS conformity: When saving FIF files to disk and the files are split into parts, the split_naming='bids' parameter now uses a “_split-%d” naming instead of the previous “_part-%d”, by Stefan Appelhoff

• Add support for whitening and multiple channel types in mne.beamformer.make_dics() by Marijn van Vliet

• Add better error message when trying to save incompatible Evoked objects to the same file by Eric Larson

• Add support for loading complex numbers from mat files by Thomas Hartmann

• Add generic reader function mne.io.read_raw() that loads files based on their extensions (it wraps the underlying specific read_raw_xxx functions) by Clemens Brunner

• Add automatic T3 magnetometer detection and application of mne.io.Raw.fix_mag_coil_types() to mne.preprocessing.maxwell_filter() by Eric Larson

• Add extended SSS (eSSS) support to mne.preprocessing.maxwell_filter() by Eric Larson

• Add 'auto' option to mne.preprocessing.ICA.find_bads_ecg() to automatically determine the threshold for CTPS method by Yu-Han Luo

• Add a notebook 3d backend for visualization in jupyter notebook with mne.viz.set_3d_backend() by Guillaume Favelier

• Add support for reading and writing surfaces in Wavefront .obj format to the mne.read_surface() and mne.write_surface() by Marijn van Vliet

• Add tutorial on how to manually fix BEM meshes in Blender by Marijn van Vliet and Ezequiel Mikulan

• mne.write_evokeds() will now accept mne.Evoked objects with differing channel orders in info['bads'], which would previously raise an exception by Richard Höchenberger

• Add support for reading channel names (e.g., for Ricoh data) to mne.io.read_raw_kit() by Alex Gramfort and Eric Larson

• The reject_tmin and reject_tmax parameters of mne.Epochs are now taken into account when using the reject_by_annotation parameter by Stefan Appelhoff

• mne.preprocessing.find_bad_channels_maxwell() now automatically applies a low-pass filter before running bad channel detection. This can be disabled, restoring previous behavior by Richard Höchenberger

• Add proj='reconstruct' to mne.Evoked.plot() and related functions to apply projectors and then undo the signal bias using field mapping by Eric Larson

• Add writing BEM surfaces and solutions in H5 format in mne.write_bem_surfaces() and mne.write_bem_solution() by Eric Larson

• When picking a subset of channels, or when dropping channels from Raw, Epochs, or Evoked, projectors that can only be applied to the removed channels will now be dropped automatically by Richard Höchenberger

• mne.Report now can add topomaps of SSP projectors to the generated report. This behavior can be toggled via the new projs argument by Richard Höchenberger

• When passing a list of Evoked objects to plot_compare_evokeds, each evoked’s .comment attribute will be used to label the trace. If .comment is empty, a 1-based index is assigned as the label by Richard Höchenberger

• Speed up mne.stats.summarize_clusters_stc() using Numba by Yu-Han Luo

• Add reject_by_annotation=True to mne.make_fixed_length_epochs() and mne.preprocessing.ICA.plot_properties() to reject bad data segments based on annotation by Yu-Han Luo

• parse_folder now accepts a path-like folder name (it used to work with strings only) by Alex Gramfort

• Add component_order parameter to mne.decoding.CSP which allows switching between mutual_info (default) and alternate (a simpler and frequently used option) by Martin Billinger and Clemens Brunner

• Add memory size information to the repr of mne.SourceSpaces and mne.SourceEstimate and related classes by Eric Larson

• Add reader for Persyst (.lay + .dat format) data in mne.io.read_raw_persyst() by Adam Li

• Use PyVista as the default backend for 3D visualization instead of Mayavi by Guillaume Favelier

• Add reader for SNIRF NIRS data in mne.io.read_raw_snirf() by Robert Luke

• Evoked has gained tmin and tmax attributes for more consistency with Epochs by Richard Höchenberger

Bugs

• Fix bug for writing and reading complex evoked data modifying mne.write_evokeds() and mne.read_evokeds() by new contributor Lau Møller Andersen

• Fix bug by adding error message when trying to save complex stc data in a non.-h5 format mne.VolSourceEstimate.save() by new contributor Lau Møller Andersen

• Fix bug with logging in mne.io.Raw.set_eeg_reference() and related functions by new contributor Simeon Wong

• Fix bug with mne.io.read_raw_gdf() where birthdays were not parsed properly, leading to an error by new contributor Svea Marie Meyer

• Fix bug with mne.io.read_raw_edf() where recording ID was not read properly for non-ASCII characters by new contributor Lx37

• Fix bug in mne.set_eeg_reference() and related functions to set info['custom_ref_applied'] to True for ‘ecog’ and ‘seeg’ channels in addition to ‘eeg’ by new contributor Liberty Hamilton

• Fix bug with mne.chpi.compute_chpi_amplitudes() and mne.chpi.filter_chpi() to optimize time window length by new contributor Steven Bierer

• Fix bug with mne.preprocessing.ICA.find_bads_eog() when more than one EOG components are present by Christian O’Reilly

• Fix bug with non-preloaded data when using raw.apply_proj().load_data().get_data() where projectors were not applied by Eric Larson

• Fix bug to permit stc.project('nn', src) to be applied after stc was restricted to an mne.Label by Luke Bloy

• Fix bug with mne.io.Raw.set_meas_date() to support setting meas_date to None, by Luke Bloy

• Fix bug with mne.setup_volume_source_space() when volume_label was supplied where voxels slightly (in a worst case, about 37% times pos in distance) outside the voxel-grid-based bounds of regions were errantly included, by Eric Larson

• Fix bug with mne coreg where reverse scalings were applied to src[0]['src_mri_t'] for volume source spaces, so morphing and plotting did not work correctly by Eric Larson

• Fix bug with mne.io.read_raw_ctf() when reference magnetometers have the compensation grade marked by Eric Larson

• Fix bug with mne.SourceSpaces.export_volume with use_lut=False where no values were written by Eric Larson

• Fix bug with mne.preprocessing.annotate_movement() where bad data segments, specified in raw.annotations, would be handled incorrectly by Luke Bloy

• Fix bug with mne.compute_source_morph() when more than one volume source space was present (e.g., when using labels) where only the first label would be interpolated when mri_resolution=True by Eric Larson

• Fix bug with mne.compute_source_morph() when morphing to a volume source space when src_to is used and the destination subject is not fsaverage by Eric Larson

• Fix bug with mne.compute_source_morph() where outermost voxels in the destination source space could be errantly omitted by Eric Larson

• Fix bug with mne.compute_source_morph() where complex data was cast to real when doing a volumetric morph by Eric Larson

• Fix bug with mne.minimum_norm.compute_source_psd_epochs() and mne.minimum_norm.source_band_induced_power() raised errors when method='eLORETA' by Eric Larson

• Fix bug with mne.minimum_norm.apply_inverse() where the explained variance did not work for complex data by Eric Larson

• Fix bug with mne.preprocessing.compute_current_source_density() where values were not properly computed; maps should now be more focal, by Alex Rockhill and Eric Larson

• Fix bug with mne.combine_evoked() where equal-weighted averages were wrongly computed as equal-weighted sums, by Daniel McCloy

• Fix bug with mne.channels.DigMontage.plot() when reference channels with no defined position are present, by Eric Larson

• Fix bug with mne.channels.read_custom_montage() where "headshape" points in SFP format were not read properly, by Eric Larson

• Fix bug with setting HTML classes when using mne.Report.add_bem_to_section by Eric Larson

• Fix bug with convex-hull based MEG helmet creation where the face area could be covered up, by Eric Larson

• Fix bug with mne.inverse_sparse.mixed_norm() and mne.inverse_sparse.gamma_map() with return_as_dipoles=True and mne.beamformer.rap_music() where dip.gof was the same for all dipoles. GOF values / explained variance across all dipoles now gets split among the dipoles using SVD of the lead fields. To get the total GOF, sum(dip.gof for dip in dipoles) can be used, by Eric Larson

• Fix bug with mne.inverse_sparse.gamma_map() where output data was not assigned properly when using a free-orientation forward and xyz_same_gamma=False by Eric Larson

• Fix to enable interactive plotting with no colorbar with mne.viz.plot_evoked_topomap() by Daniel McCloy

• Fix plotting with mne.viz.plot_evoked_topomap() to pre-existing axes by Daniel McCloy

• Fix bug with mne.viz.plot_vector_source_estimates() using the PyVista backend with time_viewer=True when updating the arrow colormaps by Eric Larson

• Fix bug with mne.viz.plot_vector_source_estimates() where clim='auto' and clim=dict(..., kind='percent') did not take into account the magnitude of the activation, by Eric Larson

• The default plotting mode for mne.io.Raw.plot() and mne browse_raw has been changed to clipping=3. to facilitate data analysis with large deflections, by Eric Larson

• PSD plots will now show non-data channels (e.g., misc) if those channels are explicitly passed to picks, by Daniel McCloy.

• Fix bug with mne.time_frequency.read_tfrs() where info['meas_date'] was not parsed correctly, by Eric Larson

• Fix bug with mne.time_frequency.tfr_array_stockwell() where inputs were not properly validated by Eric Larson

• Fix handling of NaN when using TFCE in clustering functions such as mne.stats.spatio_temporal_cluster_1samp_test() by Eric Larson

• Fix handling of signs when using TFCE by Eric Larson

• The mne.MixedSourceEstimate class has been clarified to contain two cortical surface source spaces, plus at least one other source space. Creating source estimates in other orderings is not supported, by Eric Larson

• Fix bug where VolSourceEstimate.vertices was an instance of ndarray instead of list of one ndarray, by Eric Larson

• Fix default to be foreground=None in mne.viz.plot_source_estimates() to use white or black text based on the background color by Eric Larson

• Fix bug with writing EGI and CTF mne.Info to H5 format, e.g., with mne.time_frequency.AverageTFR.save by Eric Larson

• Fix bug with topomap outlines in mne.time_frequency.AverageTFR.plot_joint() and mne.time_frequency.AverageTFR.plot_topo() by Eric Larson

• Fix bug with mne.io.Raw.plot() where toggling all projectors did not actually take effect by Eric Larson

• Fix bug with mne.write_proj() where the number of columns was incorrectly written by Eric Larson

• Fix bug with mne.read_epochs() when loading data in complex format with preload=False by Eric Larson

• Fix bug with mne.Epochs.save() where the file splitting calculations did not account for the sizes of non-data writes by Eric Larson

• Fix bug with mne.Epochs when metadata was not subselected properly when event_repeated='drop' by Eric Larson

• Fix bug with mne.Epochs where epochs.drop_log was a list of list of str rather than an immutable tuple of tuple of str (not meant to be changed by the user) by Eric Larson

• Fix bug with mne.Report where the BEM section could not be toggled by Eric Larson

• Fix bug when using mne.Epochs.crop() to exclude the baseline period would break mne.Epochs.save() / mne.read_epochs() round-trip by Eric Larson

• Fix bug with mne.Epochs.subtract_evoked where using decimated epochs would lead to an error by Eric Larson

• Fix bug with mne.viz.plot_bem() and mne.Report when plotting BEM contours when MRIs are not in standard FreeSurfer orientation by Eric Larson

• Fix bug with mne.minimum_norm.make_inverse_operator() where it would warn even when an explicit rank was used by Eric Larson

• Fix bugs with mne.beamformer.make_lcmv() and mne.beamformer.make_dics() where:

  • Noise normalization factors weight_norm='unit-noise-gain' and weight_norm='nai' were computed incorrectly

  • pick_ori='max-power' computed the max-power orientation incorrectly

  • pick_ori='normal' did not compute power or noise normalization factors correctly

  • mne.beamformer.apply_lcmv_cov() did not apply whitening and projections properly

• Fix mne setup_forward_model to have it actually compute the BEM solution in addition to creating the BEM model by Eric Larson

• Fix bug with mne.io.read_raw_edf() where null bytes were not properly handled, causing an error when opening a file by Eric Larson

• Fix bug with mne.Report() where unicode characters were not rendered properly (encoding for HTML was not set) by Eric Larson

• Fix bug with mne.preprocessing.nirs.scalp_coupling_index() where filter transition was incorrectly assigned by Robert Luke

• Fix bug with mne.make_forward_dipole() where mne.write_forward_solution() could not be used by Eric Larson

• Fix bug with mne.io.Raw.plot() when scalings='auto' where bad data would prevent channel plotting by Eric Larson

• Default border and extrapolate arguments for mne.Evoked.plot_topomap() and related functions were changed from 0. to 'mean' and 'box' to 'auto', respectively, to help more accurately reflect sensor geometries and boundary conditions. extrapolate='auto' uses extrapolate='local' for MEG data and extrapolate='head' otherwise, by Eric Larson

• Fix bug that prevents n_jobs from being a NumPy integer type, by Daniel McCloy.

• Fix bug with mne.epochs.average_movements() where epoch weights were computed using all basis vectors instead of the internal basis only by Eric Larson

• Fix bug with mne.get_volume_labels_from_aseg() where the returned labels were alphabetical instead of reflecting their volumetric ID-based order by Eric Larson

• Fix bug with mne.preprocessing.find_bad_channels_maxwell() where good data of exactly step duration would lead to an error by Eric Larson

• Fix bug with mne.preprocessing.find_bad_channels_maxwell() where indices were not handled properly when MEG channels were not first in the raw instance, and logging messages incorrectly reported the interval used by Eric Larson

• Make mne.set_config() accept path-like input values by Richard Höchenberger

• Fix bug with mne.write_labels_to_annot() and mne.datasets.fetch_hcp_mmp_parcellation() where label name strings were not properly terminated, leading to problems loading in FreeSurfer by Eric Larson

• Fix bug with mne.beamformer.make_dics() where complex conjugates were not applied properly by Britta Westner and Eric Larson

• Fix bug with mne.bem.make_watershed_bem() where the RAS coordinates of watershed bem surfaces were not updated correctly from the volume file by Yu-Han Luo

• Fix bug with mne.io.Raw.get_channel_types() and related methods where the ordering of picks was not preserved, by Eric Larson

• Fix bug with mne.io.Raw.plot_psd() with average=False and multiple channel types where channel locations were not shown properly by Eric Larson

• Fix bug with mne.viz.plot_sparse_source_estimates() when using 'sphere' mode by Eric Larson and Guillaume Favelier

• Fix bug in FieldTrip reader functions when channels are missing in the info object by Thomas Hartmann

• Throw proper error when trying to import FieldTrip Epochs data with non-uniform time for trials by Thomas Hartmann

• Throw proper error when trying to import FieldTrip data saved by an old, incompatible version by Thomas Hartmann

• Fix bug in mne.read_epochs_fieldtrip() when importing data without a trialinfo field by Thomas Hartmann

• Fix bug in mne.preprocessing.ICA.plot_properties() where time series plot doesn’t start at the proper tmin by Teon Brooks

• Fix bug with mne.preprocessing.ICA.plot_properties() where a mne.io.Raw object with annotations would lead to an error by Yu-Han Luo

• Fix bug with mne.events_from_annotations(raw.annotations) when orig_time of annotations is None and raw.first_time > 0, by Alex Gramfort

API changes

• Python 3.5 is no longer supported, Python 3.6+ is required, by Eric Larson

• adjacency has replaced connectivity in the names of:

  1. Arguments to clustering functions, such as mne.stats.permutation_cluster_test, and

  2. Function names for defining adjacency, such as mne.spatio_temporal_src_adjacency replacing mne.spatio_temporal_src_connectivity.

  The complete list of changed function names is:

  • mne.channels.find_ch_connectivity → find_ch_adjacency

  • mne.channels.read_ch_connectivity → read_ch_adjacency

  • mne.spatial_dist_connectivity → spatial_dist_adjacency

  • mne.spatial_inter_hemi_connectivity → spatial_inter_hemi_adjacency

  • mne.spatial_src_connectivity → spatial_src_adjacency

  • mne.spatial_tris_connectivity → spatial_tris_adjacency

  • mne.spatio_temporal_dist_connectivity → spatio_temporal_dist_adjacency

  • mne.spatio_temporal_src_connectivity → spatio_temporal_src_adjacency

  • mne.spatio_temporal_tris_connectivity → spatio_temporal_tris_adjacency

  “connectivity” is now reserved for discussions of functional and effective connectivity of the brain, and “adjacency” for source or sensor neighbor definitions for cluster-based analyses, by Eric Larson.

• The default for the standardize_names argument of mne.io.read_raw_kit() will change from True to False in 0.22, by Eric Larson

• The normalize_fwd argument of mne.beamformer.make_dics() has been deprecated in favor of depth, by Eric Larson

• The overwrite parameter of mne.write_bem_surfaces() and mne.write_bem_solution() defaults to True in 0.21 but will change to False in 0.22, by Eric Larson

• Add n_cols parameter to mne.preprocessing.ICA.plot_scores() to allow plotting scores in multiple columns, by Luke Bloy

• In mne.stats.permutation_cluster_test() and mne.stats.permutation_cluster_1samp_test() the default parameter value out_type='mask' has changed to None, which in 0.21 means 'mask' but will change to mean 'indices' in the next version, by Daniel McCloy

• The default window size set by filter_length when method='spectrum_fit' in mne.io.Raw.notch_filter() will change from None (use whole file) to '10s' in 0.22, by Eric Larson

• vmin and vmax parameters are deprecated in mne.Epochs.plot_psd_topomap() and mne.viz.plot_epochs_psd_topomap(); use new vlim parameter instead, by Daniel McCloy.

• The method stc_mixed.plot_surface for a mne.MixedSourceEstimate has been deprecated in favor of stc.surface().plot(...) by Eric Larson

• The method stc.normal for mne.VectorSourceEstimate has been deprecated in favor of stc.project('nn', src) by Eric Larson

• Add use_dev_head_trans parameter to mne.preprocessing.annotate_movement() to allow choosing the device to head transform is used to define the fixed cHPI coordinates by Luke Bloy

• The function mne.channels.read_dig_captrack will be deprecated in version 0.22 in favor of mne.channels.read_dig_captrak() to correct the spelling error: “captraCK” -> “captraK”, by Stefan Appelhoff

• The threshold argument in mne.preprocessing.ICA.find_bads_ecg() defaults to None in version 0.21 but will change to 'auto' in 0.22 by Yu-Han Luo

• The function mne.preprocessing.mark_flat has been deprecated in favor of mne.preprocessing.annotate_flat by Eric Larson

• The default argument meg=True in mne.pick_types() will change to meg=False in version 0.22 by Clemens Brunner

• Added mne.io.Raw.get_montage(), which obtains the montage that an instance has, by Adam Li

Authors

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

• Adam Li

• Adonay Nunes

• Alejandro Weinstein

• Alex Rockhill

• Alexandre Gramfort

• Anton Nikolas Waniek

• Britta Westner

• Christian O’Reilly

• Clemens Brunner

• Daniel McCloy

• Eric Larson

• Evgenii Kalenkovich

• Fede Raimondo

• Guillaume Favelier

• Hubert Banville

• Jeroen Van Der Donckt +

• Johann Benerradi +

• Kyle Mathewson +

• Lau Møller Andersen +

• Liberty Hamilton +

• Luke Bloy

• Lx37 +

• Mainak Jas

• Marijn van Vliet

• Martin Billinger

• Martin Schulz +

• Martin van Harmelen

• Mikolaj Magnuski

• Olaf Hauk

• Rahul Nadkarni +

• Richard Höchenberger

• Robert Luke

• Sara Sommariva

• Simeon Wong +

• Stefan Appelhoff

• Steven Bierer +

• Svea Marie Meyer +

• Teon Brooks

• Thomas Hartmann

• Yu-Han Luo

• chapochn

• mshader

Version 0.20 (2020-03-27)

Changelog

• Improved mne.viz.plot_epochs() to label epoch counts starting from 0, by Sophie Herbst

• Add minimum_norm.apply_inverse_cov() to compute static power by applying inverse solutions to a data covariance matrix by Denis Engemann, Luke Bloy, and Eric Larson

• Add mne.minimum_norm.resolution_metrics() to compute various resolution metrics for inverse solutions, by Olaf Hauk

• Add current source density mne.preprocessing.compute_current_source_density() to compute the surface Laplacian in order to reduce volume conduction in data by Alex Rockhill

• Add mne.chpi.extract_chpi_locs_ctf() to extract cHPI coil locations from CTF data by Luke Bloy

• Add mne.chpi.compute_chpi_amplitudes(), mne.chpi.compute_chpi_locs(), and mne.chpi.compute_head_pos() to compute head positions from cHPI coil locations by Eric Larson and Luke Bloy

• Add allow_line_only option to mne.chpi.filter_chpi() to allow filtering line frequencies only in files that do not have cHPI information by Eric Larson

• Add mne.io.Raw.set_meas_date() by Eric Larson

• Add mne.Epochs.as_type() to allow remapping data in MEG channels to virtual magnetometer or gradiometer channels by Sophie Herbst and Alex Gramfort

• Add copy parameter to mne.Epochs.iter_evoked() by Alex Gramfort

• Add command mne setup_source_space to quickly set up bilateral hemisphere surface-based source space with subsampling by Victor Ferat.

• Add command mne sys_info to print system information by Eric Larson

• Add function mne.make_fixed_length_epochs() to segment raw into fixed length epochs by Mohammad Daneshzand

• Add support for computing patch information only in surface source space creation with add_dist='patch' in mne.setup_source_space() and dist_limit=0 in mne.add_source_space_distances() by Eric Larson

• Add mne.Label.restrict to restrict a label to vertices within a source space by Eric Larson

• Add support for passing a destination source space src_to in mne.compute_source_morph() to ensure morphing for multiple subjects results in consistent STCs, by Eric Larson

• Add support for smooth='nearest' for surfaces in mne.compute_source_morph() by Eric Larson

• Add support for plotting fNIRS channels in mne.viz.plot_alignment(), mne.viz.plot_evoked_topo() and mne.Evoked.animate_topomap() by Eric Larson and Robert Luke

• Add command line tool mne anonymize for anonymizing raw fiff files by Luke Bloy

• Add mne.preprocessing.find_bad_channels_maxwell() for automatic bad channel detection via Maxwell filtering by Eric Larson

• Add support to mne.io.anonymize_info() to allow time offset to be applied to dates by Luke Bloy

• Add support for computing resolution matrix to get point spread functions (PSF) and cross-talk functions (CTF) in mne.minimum_norm.make_inverse_resolution_matrix(), mne.beamformer.make_lcmv_resolution_matrix(), mne.minimum_norm.get_cross_talk(), mne.minimum_norm.get_point_spread() by Olaf Hauk

• Add mne.preprocessing.read_ica_eeglab() to read EEGLAB ICA decompositions by Christian O’Reilly

• Add keyboard functionality to interactive colorbar plotting TFRs by Stefan Repplinger

• Add the ability to return_event_id in mne.read_events() for use with MNE-C produced -annot.fif files, by Eric Larson

• Add option to mne.connectivity.spectral_connectivity to compute corrected imaginary PLV by Adonay Nunes

• Add mne.SourceEstimate.estimate_snr() to estimate source-space SNR, by Kaisu Lankinen and Padma Sundaram

• Add option to specify the coordinate frame in mne.channels.read_custom_montage() by Eric Larson

• Add option to use match_case=False to mne.io.Raw.set_montage() and related functions by Eric Larson

• Add reader for NIRx data in mne.io.read_raw_nirx() by Robert Luke

• Add function to convert NIRS data to optical density mne.preprocessing.nirs.optical_density() by Robert Luke

• Add function to convert NIRS data to haemoglobin concentration mne.preprocessing.nirs.beer_lambert_law() by Robert Luke

• Add fig argument to mne.viz.plot_evoked_field() by Eric Larson

• Add functions to calculate spatial information of NIRS channels mne.preprocessing.nirs.source_detector_distances() and mne.preprocessing.nirs.short_channels() by Robert Luke

• Add reader for *.dat electrode position files mne.channels.read_dig_dat() by Christian Brodbeck

• Improved mne.viz.plot_events() to always show event counts by Eric Larson

• Improved LIMO Dataset usage and example for usage of mne.stats.linear_regression() by Jose Alanis

• Add support for reduce_rank=True for vector beamformers by Eric Larson

• Add method='sphere' support for using Freesurfer spherical inflation in mne.decimate_surface() to facilitate mesh downsampling for use with mne.make_bem_model() by Eric Larson

• Speed up mne.beamformer.make_lcmv() and mne.beamformer.make_dics() calculations by vectorizing linear algebra calls by Dmitrii Altukhov and Eric Larson

• Speed up mne.make_forward_solution() using Numba, by Eric Larson

• Speed up mne.io.read_raw_fif() data reading when the recording is long and there are many data tags repeatedly accessed, by Eric Larson

• For KIT systems without built-in layout, mne.channels.find_layout() now falls back on an automatically generated layout, by Christian Brodbeck

• mne.Epochs.plot() now takes a epochs_colors parameter to color specific epoch segments by Mainak Jas

• Add command mne setup_forward_model to quickly create a BEM model for a subject by Victor Ferat.

• Add command mne prepare_bem_model to quickly create a BEM solution using the linear collocation approach by Victor Ferat.

• Add support for reading .bdip Xfit binary dipole fit files in mne.read_dipole() by Eric Larson

• Allow returning vector source estimates from sparse inverse solvers through pick_ori='vector' by Christian Brodbeck

• Add NIRS support to mne.viz.plot_topomap() and mne.viz.plot_ica_components() by Robert Luke

• Add the ability to mne.channels.equalize_channels() to also re-order the channels and also operate on instances of mne.Info, mne.Forward, mne.Covariance and mne.time_frequency.CrossSpectralDensity by Marijn van Vliet

• Allow mne.channels.read_custom_montage to handle fiducial points for BESA spherical (.elp) files by Richard Höchenberger

• Add rank argument to mne.fit_dipole() by Eric Larson

• Add function to convert events to annotations mne.annotations_from_events() by Nicolas Barascud

• Add function to calculate scalp coupling index for fNIRS data mne.preprocessing.nirs.scalp_coupling_index() by Robert Luke

• Add item argument to mne.Epochs.get_data() for faster access to NumPy data arrays compared to mne.Epochs.__getitem__() for frequent access on large mne.Epochs objects, by Eric Larson

• More accurate coordinate system for Easycap montages in mne.channels.make_standard_montage() by Christian Brodbeck

• Add border argument to mne.viz.plot_topomap(). border controls the value of the edge points to which topomap values are extrapolated. border='mean' sets these points value to the average of their neighbours. By Mikołaj Magnuski

• Add function mne.viz.link_brains() to link time properties of multiple brain objects interactively by Guillaume Favelier

• Add function mne.preprocessing.annotate_movement() to annotate periods with head motion and mne.preprocessing.compute_average_dev_head_t() to re-estimate the device to head transform with average head position during segments with acceptable head movement. by Adonay Nunes

• Make selected channels more distinguishable in mne.Epochs.plot_sensors() when using kind='select' by Mikołaj Magnuski

• Allow retrieval of the number of Infomax ICA iterations via the new return_n_iter keyword argument of mne.preprocessing.infomax() by Richard Höchenberger

• Expose the number of ICA iterations during the fitting procedure via the n_iter_ attribute of mne.preprocessing.ICA by Richard Höchenberger

• mne.grand_average() now produces a warning when only a single dataset was passed, instead of raising an error by Richard Höchenberger

• Add nrows and ncols parameters to mne.viz.plot_evoked_topomap(), which allows to create multiline topomap plots for Evoked. By Federico Raimondo

• Improve repr of mne.Info (empty items are not shown anymore) by Clemens Brunner

Bug

• Fix the reduce_rank parameter in mne.beamformer.make_lcmv() and mne.beamformer.make_dics() to reduce the rank of the leadfield first before then reducing the rank of the denominator of the beamformer formula for the inversion by Britta Westner and Eric Larson.

• Fix bug with mne.beamformer.make_lcmv() with data where rank was incorrectly checked by Eric Larson.

• Allow mne.channels.read_dig_hpts() to accept point categories (eg. EEG) to be specified in upper case by Alex Gramfort.

• Fix a bug in mne.MixedSourceEstimate.plot_surface that prevented plotting in latest PySurfer by Christian O’Reilly.

• Fix method='eLORETA' in mne.minimum_norm.apply_inverse(), by Eric Larson:

  1. regularization, which was off by roughly a factor of a square root

  2. units, which are now nAm instead of being arbitrary

  3. explained variance and residuals, which were previously unavailable

  4. force_equal in the case of loose orientations, which previously defaulted to True now defaults to False. Reapplying orientation priors at each iteration of the algorithm sufficiently preserves a smooth transition between loose=0. to loose=1. without compromising localization accuracy in testing.

• Fix bug in method='eLORETA' for mne.minimum_norm.apply_inverse() (and variants) to allow restricting source estimation to a label by Luke Bloy

• Fix bug in mne.compute_covariance() and mne.compute_raw_covariance() where biased normalization (based on degrees of freedom) was used and cov.nfree was not set properly by Eric Larson

• Fix mne.VectorSourceEstimate.normal to account for cortical patch statistics using use_cps=True by Eric Larson

• Fix pick_ori='normal' for mne.minimum_norm.apply_inverse() when the inverse was computed with loose=1. and the forward solution was not in surface orientation, by Eric Larson

• Fix missing xlabel for mne.io.Raw.plot_psd() and similar functions when passing a subset of axes from a figure by Alex Gramfort

• Fix wrong DataFrame index when index=None in methods mne.io.Raw.to_data_frame(), mne.Epochs.to_data_frame(), mne.Evoked.to_data_frame(), and mne.SourceEstimate.to_data_frame(), by Daniel McCloy.

• Fix incorrect scaling of cluster temporal extent in mne.stats.summarize_clusters_stc() by Daniel McCloy.

• Fix mne.time_frequency.read_tfrs() to properly read Info transforms by Eric Larson

• Fix mne.viz.plot_sensors() to always plot in head coordinate frame by Daniel McCloy.

• Fix mne.io.read_raw_cnt() for version 1 of format in the presence of annotations by Alex Gramfort.

• Fix mne.decoding.GeneralizingEstimator and related classes to support multi-class sklearn scorers such as 'roc_auc_ovo' and 'roc_auc_ovo_weighted' by Eric Larson

• Fix mne.io.read_raw_ctf() to set measurement date from CTF ds files by Luke Bloy.

• Fix mne.read_epochs_eeglab() that ignored channel locations by Alex Gramfort.

• Fix mne.io.read_raw_brainvision() when channel names have spaces by Sebastian Major.

• Fix mne.io.read_raw_brainvision() when "Core" is in the data header by Eric Larson

• Fix mne.io.Raw.anonymize() to correctly reset raw.annotations.orig_time by Luke Bloy.

• Fix mne.io.Raw.anonymize() to correctly avoid shifting raw.annotations.onset relative to raw.first_samp by Eric Larson

• Fix mne.io.Raw.set_channel_types() and mne.io.Raw.rename_channels() and related methods to return the instance instead of None by Eric Larson

• mne.Epochs.iter_evoked() now does not return a copy of info when copy=False (default parameter) by Alex Gramfort

• The attribute mne.Annotations.orig_time is now read-only, and is a datetime object (or None) rather than float, by Eric Larson

• Fix bug where MRI distances were not properly initialized in mne coreg by Eric Larson

• Fix xscale='log' in mne.io.Raw.plot_psd() and related functions by Alex Gramfort

• Unify behavior of raw.annotations.append(...) when raw.info['meas_date'] is None to make onsets absolute relative to first_samp as they are when raw.info['meas_date'] is not None; i.e., you might need to do raw.annotations.append(old_time + raw.first_time), by Eric Larson

• The info['meas_date'] entry is now a datetime object (or None) rather than float, by Eric Larson

• Fix mne.time_frequency.AverageTFR.save() and related functions to deal with datetime objects properly by Eric Larson

• Fix date reading before Unix time zero (1970 Jan 1) on Windows by Alex Rockhill.

• Fix bug running subprocesses (e.g., in mne.bem.make_watershed_bem()) in Jupyter notebooks, by Eric Larson

• Fix mne.io.read_raw_artemis123() to add HPI locations to digitization points, by Luke Bloy

• Fix mne.Epochs.shift_time() and mne.Evoked.shift_time() to return the modified Epochs or Evoked instance (instead of None) by Daniel McCloy.

• Fix mne.read_annotations() for text files with zero or one annotations, by Adonay Nunes

• Fix bug in ICA where requesting extended infomax via fit_params={'extended': True} was overridden, by Daniel McCloy.

• Fix bug in mne.Epochs.interpolate_bads() where the origin was not used during MEG or EEG data interpolation by Eric Larson. Old behavior can be achieved using origin=(0., 0., 0.) for EEG and origin=(0., 0., 0.04) for MEG, and the new default is origin='auto', which uses a head-digitization-based fit.

• Fix bug in mne.write_evokeds() where evoked.nave was not saved properly when multiple Evoked instances were written to a single file, by Eric Larson

• Fix bug in mne.preprocessing.mark_flat where acquisition skips were not handled properly, by Eric Larson

• Fix bug in mne.viz.plot_bem() where some sources were not plotted by Jean-Remi King and Eric Larson

• Fix TAL channel parsing (annotations) for EDF-D files by Clemens Brunner

• Fix bug with mne.viz.plot_dipole_locations() when plotting in head coordinates by Eric Larson

• Fix handling in cases where no components are found in mne.preprocessing.corrmap() by Eric Larson

• Fix handling of repeated events in mne.Epochs by Fahimeh Mamashli and Alex Gramfort

• Fix many bugs with plotting sensors overlaid on a head outline. All plotting is now done in head coordinates and scaled by head_radius, which defaults to 0.095, by Eric Larson

• Fix mne.io.anonymize_info() to allow shifting dates of service and to match anticipated changes in mne-cpp by Luke Bloy

• Fix reading of cardinals in .htps files (identifier are int not strings) by Alex Gramfort

• Fix IO of TFRs when event_id contain a / in one of the keys by Alex Gramfort

• Fix plotting of TFRs with linear y-scale (misaligned frequency bins), by Stefan Repplinger and Eric Larson

• Fix info['sfreq'] when decimating in mne.time_frequency.tfr_multitaper() and mne.time_frequency.tfr_morlet() and make sure an error is raised when exceed Nyquist frequency by Adonay Nunes

• Fix bug in EDF(+) loading, filter values ignored by insufficient regex, by Demetres Kostas

• Fix missing scaling of tolerance parameter in mne.inverse_sparse.tf_mixed_norm() and mne.inverse_sparse.mixed_norm(), by Mathurin Massias

• Fix the automatic scaling of the glyphs in mne.viz.plot_vector_source_estimates() by using 10% of the brain width, by Guillaume Favelier

• Fix handling of missing values (NaNs) in mne.time_frequency.psd_welch by Clemens Brunner

• Fix mne.decoding.LinearModel to support the refitted estimator of GridSearchCV in sklearn by Chun-Hui Li

• Fix mne.viz.plot_topomap() when there are bad channels in the provided mne.Info instance by Eric Larson

• Fix check for subject definition existing in source space in mne.compute_source_morph() and related functions by Eric Larson

• Fix creation of new figures in mne.Epochs.plot_image() and mne.viz.plot_epochs_image() by Eric Larson

• Fix bug in Xdawn where filters where selected along the incorrect axis, by Henrich Kolkhorst

• Fix bug in mne.bem.make_watershed_bem() where some surfaces were saved incorrectly in the working directory by Yu-Han Luo

• Fix support for multiple TAL (annotations) channels in BDF reader by Clemens Brunner

• Fix missing brainmask file type in mne.bem.make_watershed_bem() by changing its default value to ws.mgz by Fu-Te Wong

• Fix bug in mne.channels.make_standard_montage() which would return easycap-M1 even when requesting easycap-M10 by Christian Brodbeck

• Fix the way planar gradiometers are combined in mne.viz.plot_tfr_topomap() and mne.Epochs.plot_psd_topomap() by Geoff Brookshire

• Improve error message when trying to load FieldTrip data from a cell array by Thomas Hartmann

• Fix bug in mne.read_evoked_fieldtrip() causing it to crash when channels were present in the provided Info object but were not present in the data by Thomas Hartmann

• Fix placement of extrapolation points in mne.Evoked.plot_topomap() and related functions when exactly three channels were used by Mikołaj Magnuski.

• Fix bug in reading annotations in read_annotations(), which would not accept “;” character by Adam Li

• Fix bug in mne.Report.parse_folder(), which would not recognize *meg.fif files by Dmitrii Altukhov.

• Include fit_params when saving an ICA instance to disk by Richard Höchenberger

• Update old url link in mne.datasets.eegbci.load_data() to EEGMI_URL = 'https://physionet.org/files/eegmmidb/1.0.0/' by Ramiro Gatti

• Ensure corrected p-values calculated by mne.stats.bonferroni_correction() never exceed the value of 1.0 by Richard Höchenberger

API

• mne.io.pick.get_channel_types is now called mne.io.pick.get_channel_type_constants to better reflect its return values, by Daniel McCloy.

• mne.Evoked.as_type() now returns an instance of mne.EvokedArray by Sophie Herbst and Alex Gramfort

• Bumped minimum requirements to fall 2017 versions by Eric Larson:

  • NumPy 1.13.3

  • SciPy 1.0.0

  • matplotlib 2.1

  • scikit-learn 0.19.1 (optional requirement)

  • pandas 0.21 (optional requirement)

• mne.Epochs.plot() now accepts an event_id parameter (useful in tandem with event_colors for specifying event colors by name) by Daniel McCloy.

• Passing ch_types=None has been deprecated in favor of explicitly passing ch_types='misc' in mne.create_info() by Eric Larson

• New time conversion options for methods mne.io.Raw.to_data_frame(), mne.Epochs.to_data_frame(), mne.Evoked.to_data_frame(), and mne.SourceEstimate.to_data_frame(), by Daniel McCloy.

• mne.Epochs.shift_time() and mne.Evoked.shift_time() now allow shifting times by arbitrary amounts (previously only by integer multiples of the sampling period), by Daniel McCloy and Eric Larson.

• The head_pos argument of mne.Evoked.plot_topomap() and related functions has been deprecated in favor of head_radius, by Eric Larson.

• The layout argument to topomap-related functions such as mne.Evoked.plot_topomap() and mne.viz.plot_tfr_topomap() has been deprecated in favor of channel-position based flattening based on the info and sphere argument, by Eric Larson.

• The APIs of mne.io.Raw.plot_projs_topomap(), mne.Epochs.plot_projs_topomap() and mne.Evoked.plot_projs_topomap() are now more similar to mne.viz.plot_projs_topomap() by Daniel McCloy.

• The function mne.setup_volume_source_space() has a sphere_units argument that defaults to 'mm' in 0.20 but will change to 'm' in 0.21, set it to avoid a warning by Eric Larson.

• mne.viz.plot_projs_topomap() and the related methods mne.io.Raw.plot_projs_topomap(), mne.Epochs.plot_projs_topomap() and mne.Evoked.plot_projs_topomap() now accept parameter vlim to control the colormap, with keyword 'joint' computing the colormap jointly across all projectors of a given channel type, by Daniel McCloy.

• New methods mne.io.Raw.get_channel_types(), mne.Epochs.get_channel_types(), mne.Evoked.get_channel_types() by Daniel McCloy.

• Deprecate mne.minimum_norm.point_spread_function and mne.minimum_norm.cross_talk_function by Alex Gramfort

• Deprecate montage parameter of mne.create_info() in favor of mne.io.Raw.set_montage(), mne.Info.set_montage(), and related functions by Eric Larson

• mne.channels.equalize_channels() no longer operates in-place by default, but instead makes copies of the objects when necessary (see copy parameter) by Marijn van Vliet

• mne.channels.equalize_channels() now uses the first object in the list as a template for channel ordering by Marijn van Vliet

• mne.channels.equalize_channels() now also re-orders the channels to match, in addition to dropping channels that are not shared by all objects by Marijn van Vliet

• mne.io.Raw.pick_channels(), mne.Epochs.pick_channels() and mne.Evoked.pick_channels() now have an ordered parameter to enforce the ordering of the picked channels by Marijn van Vliet

• New methods mne.Forward.pick_channels(), mne.Covariance.pick_channels(), mne.Info.pick_channels, mne.time_frequency.CrossSpectralDensity.pick_channels() by Marijn van Vliet

• New attributes mne.Forward.ch_names and mne.Info.ch_names by Marijn van Vliet

• In Xdawn, the components are stored in the rows of attributes filters_ and patterns_ to be consistent with CSP and ICA by Henrich Kolkhorst

• Drop unit keyword argument from mne.channels.read_custom_montage(), as it was unused by Richard Höchenberger

• Deprecate mne.preprocessing.run_ica, use mne.preprocessing.ICA.detect_artifacts instead by Richard Höchenberger

Authors

People who contributed to this release (in alphabetical order):

• Adam Li

• Adonay Nunes

• Alex Rockhill

• Alexandre Gramfort

• Ariel Rokem

• Britta Westner

• Carlos de la Torre

• Christian Brodbeck

• Christian O’Reilly

• Chun-Hui Li

• Clemens Brunner

• Daniel McCloy

• Demetres Kostas

• Denis A. Engemann

• Dmitrii Altukhov

• Dominik Welke

• Eric Larson

• Ezequiel Mikulan

• Fahimeh Mamashli

• Fede Raimondo

• Fu-Te Wong

• Geoff Brookshire

• Guillaume Favelier

• Henrich Kolkhorst

• Joan Massich

• José C. García Alanis

• Jussi Nurminen

• Kaisu Lankinen

• Luke Bloy

• Mainak Jas

• Marijn van Vliet

• Mathurin Massias

• Mikolaj Magnuski

• Mohamed Sherif

• Mohammad Daneshzand

• Nataliia Kozhemiako

• Nicolas Barascud

• Nicolas Legrand

• Olaf Hauk

• Padma Sundaram

• Ramiro Gatti

• Richard Höchenberger

• Robert Luke

• Robert Oostenveld

• Sebastian Major

• Sophie Herbst

• Stefan Appelhoff

• Stefan Repplinger

• Thomas Hartmann

• Victor Férat

• Yu-Han Luo

Version 0.19 (2019-09-24)

Changelog

• Add mne.cuda.set_cuda_device() and config variable MNE_CUDA_DEVICE to select among multiple GPUs (by numeric device ID) by Daniel McCloy.

• Add mne.channels.make_standard_montage() to create mne.channels.DigMontage from templates by Joan Massich and Alex Gramfort.

• Add mne.channels.compute_dev_head_t() to compute Device-to-Head transformation from a montage by Joan Massich and Alex Gramfort.

• Add mne.channels.read_dig_fif() to read digitization coordinates from .fif files by Joan Massich and Alex Gramfort.

• Add mne.channels.read_dig_egi() to read digitization coordinates from EGI .xml files by Joan Massich and Alex Gramfort.

• Add mne.channels.read_dig_polhemus_isotrak() and mne.channels.read_polhemus_fastscan() to read Polhemus data by Joan Massich

• Add mne.channels.read_dig_captrack to read BrainVision CapTrak (BVCT) digitization coordinate files by Stefan Appelhoff and Joan Massich

• Add mne.channels.make_dig_montage() to create mne.channels.DigMontage objects out of np.arrays by Joan Massich

• Add mne.channels.read_custom_montage() to read various EEG electrode locations files by Joan Massich and Alex Gramfort.

• Add support for making epochs with duplicated events, by allowing three policies: “error” (default), “drop”, or “merge” in mne.Epochs by Stefan Appelhoff

• Allow mne.Annotations.crop() to support negative tmin and tmax by Joan Massich

• Unknown events code in GDF are now visible in the event_id by Theodore Papadopoulo

• Now mne.io.read_raw_ctf() populates raw.annotations with the markers in MarkerFile.mrk if any by Joan Massich

• Add options for controlling the use of the -T1 flag and the location of the brainmask output in mne watershed_bem by Eric Larson

• Add support to mne.read_annotations() to read CTF marker files by Joan Massich

• Do not convert effective number of averages (nave attribute of mne.Evoked) to integer except when saving to FIFF file by Daniel McCloy.

• Add automatic fiducial position estimation in mne coreg using MNI Talairach fiducial locations in mne.coreg.get_mni_fiducials() by Jon Houck and Eric Larson

• Add support for mne coreg scaling surrogate subjects without surface reconstructions, such as those created for volumetric analyses only (e.g., with recon-all -autorecon1) by Eric Larson

• Add reader for Curry data in mne.io.read_raw_curry() by Dirk Gütlin

• Butterfly channel plots now possible for mne.Epochs.plot_psd() with average=False. Infrastructure for this function now shared with analogous Raw function, found in mne.viz.utils by Jevri Hanna

• Add option not to orthogonalize power envelopes with orthogonalize=False in mne.connectivity.envelope_correlation by Denis Engemann

• Accept filenames of raw .fif files that end in _meg.fif to enable complicance with the Brain Imaging Data Structure by Stefan Appelhoff

• Add function to check the type of a FIF file using mne.what() and mne what by Eric Larson

• Add support for specifying the initial time and/or position and providing a mne.SourceMorph instead of mne.SourceSpaces in mne.viz.plot_volume_source_estimates() by Eric Larson

• Speed up morph map generation in mne.read_morph_map() by ~5-10x by using numba.jit() by Eric Larson

• Speed up mne.setup_volume_source_space(), especially when volume_label is not None by Eric Larson

• Speed up mne coreg interactive and automated (ICP) alignment by using nearest-neighbor calculations in the MRI coordinate frame, by Eric Larson

• Add mne.dig_mri_distances() to compute the distances between digitized head points and the MRI head surface by Alex Gramfort and Eric Larson

• Add scale bars for data channels in mne.io.Raw.plot() by Eric Larson

• Add mne.viz.plot_brain_colorbar() to plot a colorbar appropriately matched to a mne.viz.plot_source_estimates() plot by Eric Larson

• Add support for showing head surface (to visualize digitization fit) while showing a single-layer BEM to mne.viz.plot_alignment() by Eric Larson

• Add option include_tmax=True to cropping methods mne.io.Raw.crop(), mne.Epochs.crop(), mne.Evoked.crop(), mne.SourceEstimate.crop(), mne.Dipole.crop(), and mne.time_frequency.AverageTFR.crop() by Eric Larson

• Change the behavior of mne.io.Raw.plot() for scalings='auto' and remove_dc=True to compute the scalings on the data with DC removed by Clemens Brunner

• Allow creating annotations within existing annotations in mne.io.Raw.plot() by default (the old snapping behavior can be toggled by pressing ‘p’) by Clemens Brunner

• Add plotting of rank estimates in mne.viz.plot_cov() by Eric Larson

• Add a new mne.viz.plot_sensors_connectivity function to visualize the sensor connectivity in 3D by Guillaume Favelier and Alex Gramfort

• Add support for info['utc_offset'], info['device_info'], and info['helium_info'] components of mne.Info by Eric Larson

• Add control over dipole colors in mne.viz.plot_dipole_locations() when using orthoview mode by Eric Larson

• Use second-order-sections filtering in mne.io.Raw.plot() and mne browse_raw by Eric Larson

• Add re-referencing functionality for ecog and seeg channel types in mne.set_eeg_reference() by Keith Doelling

• Add support for median averaging and for returning unaggregated segments in mne.time_frequency.psd_welch by Richard Höchenberger

• io.read_raw_kit(): add support for NYU New York 2019 system update, by Christian Brodbeck

Bug

• Fix setting montage eeg ref position for captrak by Joan Massich

• Fix saving raw read from BDF file using tmin and tmax using preload=False by Alex Gramfort

• Fix mne.grand_average() to use equal sum-to-one weights (like it used to, before changes to underlying mne.combine_evoked()) by Daniel McCloy

• Fix mne.io.Raw.filter() to deal with instances with no data channels properly by Eric Larson

• Fix one-sample baseline issue in mne.BaseEpochs when using tmin=0 by Milan Rybář

• Fix bug in mne.viz.plot_volume_source_estimates() where 'glass_brain' MRIs were not transformed to MNI space, by Eric Larson

• Fix bug in mne.viz.plot_volume_source_estimates() where MRIs with voxels not in RAS orientation could not be browsed properly, by Eric Larson

• Fix bug in mne.SourceMorph.apply() where output STCs had stc.vertices defined improperly, by Eric Larson

• Fix bug in mne.SourceMorph.apply() where the default was errantly mri_space=False instead of mri_space=None (as documented), by Eric Larson

• Fix mne.VolVectorSourceEstimate.normal and mne.minimum_norm.apply_inverse() to only allow normal extraction/orientation for surface and discrete source spaces by Eric Larson

• Fix mne.io.Raw.set_annotations() for meas_date previous to 1970 by Joan Massich

• Fix horizontal spacing issues in mne.io.Raw.plot_psd() by Jevri Hanna

• Fix reading of dates in BrainVision files if no “New Segment” marker is specified, no date is given, or data is missing, by Stefan Appelhoff

• Fix bug with reading one-channel GDF files by Abram Hindle

• Fix bug with y-axis labeling in mne.io.Raw.plot_psd() by Eric Larson

• Fix side-effect where mne.viz.plot_ica_sources() and mne.preprocessing.ICA.plot_sources() changed the ICA.exclude attribute even when users didn’t interact with the plot by Daniel McCloy.

• Fix scaling of sources in ica.plot_sources(epochs) by Eric Larson

• Fix wrong assumptions about units in BrainVision montages and add test asserting units in “mm” or “auto”, by Stefan Appelhoff

• Fix scaling issue with signals in mV in EDF files read with mne.io.read_raw_edf() by Alex Gramfort

• Fix mne.extract_label_time_course() behavior when using STCs generated with apply_inverse(..., label=label) or stc.in_label by Eric Larson

• Fix bug in mne.io.read_raw_brainvision() so that recording date timestamps are also recognized if channel reference data is negative, by Stefan Appelhoff

• Fix order of info['dig'] that was alphabetical based on channel names and not following the channel order when using mne.io.Raw.set_montage() and a mne.channels.Montage object by Joan Massich and Alex Gramfort.

• Fix reading CNT files larger than 2Gb by Joan Massich

• Fix reading of 4D/BTi data with different channel names and onsets in mne.io.read_raw_bti() by Joshua Bear and Eberhard Eich

• Fix formula for effective number of averages in mne.combine_evoked() when weights='equal' by Daniel McCloy.

• Fix bug in mne.simulation.simulate_stc() to avoid empty stc if label vertices and source space do not intersect, by Kostiantyn Maksymenko

• Fix event_id='auto' in mne.events_from_annotations() to recover Brainvision markers after saving it in .fif by Joan Massich

• Fix mne.read_epochs_eeglab() when epochs are stored as float. By Thomas Radman

• Fix mne.Evoked.resample() and mne.Epochs.resample() not setting inst.info['lowpass'] properly by Eric Larson

• Fix checks when constructing volumetric and surface source spaces with mne.setup_volume_source_space() and mne.setup_source_space(), respectively, by Eric Larson

• Fix bug in handling of mne.Evoked types that were not produced by MNE-Python (e.g., alternating average) by Eric Larson

• Fix bug in mne.read_source_estimate() where vector volumetric source estimates could not be read by Eric Larson

• Fix bug in mne.inverse_sparse.mixed_norm() and mne.inverse_sparse.tf_mixed_norm() where weights was supplied but weights_min was not, by Eric Larson

• Fix bug in mne.set_eeg_reference() where non-EEG channels could be re-referenced by default if there were no EEG channels present, by Eric Larson

• Fix bug in mne.io.Raw.plot() when using HiDPI displays and the MacOSX backend of matplotlib by Eric Larson

• Fix bug in mne.viz.plot_compare_evokeds() when using Neuromag 122 system by Eric Larson

• Fix bug in mne.Epochs.plot_psd() when some channels had zero/infinite psd values causing erroneous error messages by Luke Bloy

• Fix mne.Evoked.decimate() not setting inst.first and inst.last properly by Marijn van Vliet

• Fix mne.io.read_raw_brainvision() not handling Event markers created by PyCorder correctly by Richard Höchenberger

• Fix support for string-like objects (such as pathlib.Path) by Eric Larson

• Fix mne.Report silently suppressing exceptions when used as a context manager by Marijn van Vliet

API

• Deprecate mne.channels.Montage class, mne.channels.read_montage and mne.channels.read_dig_montage function by Joan Massich.

• Deprecate passing Montage, str as montage parameter in mne.io.Raw.set_montage() by Joan Massich.

• Deprecate set_dig parameter in mne.io.Raw.set_montage() and update_ch_names in mne.io.RawEEGLAB.set_montage when using mne.channels.DigMontage as by Joan Massich.

• Now mne.io.Raw.set_montage() raises an error when mne.channels.DigMontage contains only a subset of the channels in raw.info. It also adds raise_if_subset parameter to ensure backward compatibility (defaults to False in 0.19, to True in 0.20, and will be removed in 0.21) by Joan Massich.

• Minimum dependency versions for the following libraries have been bumped up (by Eric Larson):

  • NumPy: 1.12.1

  • SciPy: 0.18.1

  • matplotlib: 2.0.2

  • scikit-learn: 0.18.2

  • pandas 0.19.2

• New boolean parameter show_scrollbars for mne.io.Raw.plot(), mne.Epochs.plot(), and mne.preprocessing.ICA.plot_sources() (and associated functions) that allows hiding the scrollbars and buttons for a “zen mode” data browsing experience. When the plot window has focus, zen mode can be toggled by pressing z, by Daniel McCloy.

• Deprecate mne.evoked.grand_average in favor of mne.grand_average() (which works on both Evoked and AverageTFR) by Daniel McCloy

• Deprecate exclude parameter in mne.viz.plot_ica_sources() and mne.preprocessing.ICA.plot_sources(), instead always use the exclude attribute of the ICA object by Daniel McCloy.

• Deprecate montage parameter in favor of the set_montage method in all EEG data readers mne.io.read_raw_cnt(), mne.io.read_raw_egi(), mne.io.read_raw_edf(), mne.io.read_raw_gdf(), mne.io.read_raw_nicolet(), mne.io.read_raw_eeglab() and mne.read_epochs_eeglab() by Alex Gramfort

• New parameter clear in mne.viz.plot_epochs_image() for clearing pre-existing axes before plotting into them by Daniel McCloy

• mne.viz.plot_epochs_image() no longer supports group_by='type' — combining by channel type is now the default when picks is a channel type string; to get individual plots for each channel, pass picks as a list of channel names or indices by Daniel McCloy

• New parameter combine in mne.viz.plot_compare_evokeds() for specifying method to combine information across channels by Daniel McCloy

• FIFF constants related to SmartShield (*_SMSH_* and *_SMARTSHIELD) have been renamed to IAS for consistency with MEGIN, by Eric Larson

• The gfp parameter of mne.viz.plot_compare_evokeds() is deprecated; use combine='gfp' instead by Daniel McCloy

• The truncate_yaxis='max_ticks' parameter of mne.viz.plot_compare_evokeds() is deprecated; use truncate_yaxis='auto' instead by Daniel McCloy

• The truncate_xaxis and truncate_yaxis parameters of mne.viz.plot_compare_evokeds() now perform one-sided truncation unless both are True by Daniel McCloy

• The show_legend parameter of mne.viz.plot_compare_evokeds() is renamed to legend by Daniel McCloy

• mne.viz.plot_compare_evokeds() always returns a list of figures even when a single figure is generated by Daniel McCloy

• Deprecate average=True and spatial_colors=False for mne.Epochs.plot_psd() by Jevri Hanna

• mne.io.read_raw_brainvision() no longer raises an error when there are inconsistencies between info['chs'] and montage but warns instead by Joan Massich

• Add update_ch_names parameter to mne.io.RawEEGLAB.set_montage to allow updating the channel names based on the montage by Joan Massich

• Reading annotations contained in GDF files with mne.io.read_raw_gdf() now returns numeric event codes as descriptions (instead of textual descriptions) due to restrictive licensing of the GDF event code table from BioSig by Clemens Brunner

• channels.find_ch_connectivity now returns pre-built neighbor maps for KIT systems when available, by Christian Brodbeck

Version 0.18 (2019-05-19)

Changelog

• Add event_id='auto' in mne.events_from_annotations() to accommodate Brainvision markers by Jona Sassenhagen, Joan Massich and Eric Larson

• Add example on how to simulate raw data using subject anatomy, by Ivana Kojcic,`Eric Larson`_,`Samuel Deslauriers-Gauthier`_ and`Kostiantyn Maksymenko`_

• mne.beamformer.apply_lcmv_cov() returns static source power after supplying a data covariance matrix to the beamformer filter by Britta Westner and Marijn van Vliet

• Add butterfly and order arguments to mne.viz.plot_epochs() and offer separated traces for non-meg data (seeg, eeg, ecog) in butterfly view by Stefan Repplinger and Eric Larson

• mne.Epochs.get_data() now takes a picks parameter by Jona Sassenhagen

• plot_compare_evokeds() will generate topo plots if axes='topo' by Jona Sassenhagen

• mne.viz.iter_topography can yield an additional axis, e.g., for plotting legends by Jona Sassenhagen and Daniel McCloy

• Default plot title reflects channel type when picks is a channel type in plot_compare_evokeds() by Daniel McCloy

• Color scale limits in plot_topo_image_epochs() are now computed separately per channel type in combined mag/grad plots, by Daniel McCloy

• mne.simulation.simulate_stc() now allows for label overlaps by Nathalie Gayraud, and Ivana Kojcic

• Add long_format option to the pandas dataframe exporters, e.g mne.Epochs.to_data_frame() by Denis Engemann

• Add example on how to load standard montage Plotting sensor layouts of EEG systems by Joan Massich

• Add new tutorial on EEG forward operator with a template MRI by Alex Gramfort, and Joan Massich

• Add mne.Epochs.apply_hilbert() and mne.Evoked.apply_hilbert() by Eric Larson

• Add convenience fsaverage subject dataset fetcher / updater mne.datasets.fetch_fsaverage() by Eric Larson

• Add fmin and fmax argument to mne.time_frequency.AverageTFR.crop() and to mne.time_frequency.EpochsTFR.crop() to crop TFR objects along frequency axis by Dirk Gütlin

• Add support to mne.read_annotations() to read CNT formats by Joan Massich

• Add reject parameter to mne.preprocessing.ICA.plot_properties() to visualize rejected epochs by Antoine Gauthier

• Add support for picking channels using channel name and type strings to functions with picks arguments, along with a convenience mne.io.Raw.pick(), mne.Epochs.pick(), and mne.Evoked.pick() method, by Eric Larson

• Add new tutorial on Sleep stage classification from polysomnography (PSG) data by Alex Gramfort, Stanislas Chambon and Joan Massich

• Add data fetchers for polysomnography (PSG) recordings from Physionet (mne.datasets.sleep_physionet.age.fetch_data() and mne.datasets.sleep_physionet.temazepam.fetch_data()) by Alex Gramfort and Joan Massich

• Add envelope correlation code in mne.connectivity.envelope_correlation by Denis Engemann, Sheraz Khan, and Eric Larson

• Add option to toggle all projectors in mne.io.Raw.plot() and related functions by Eric Larson

• Add support for indexing, slicing, and iterating mne.Annotations by Joan Massich

• mne.io.Raw.plot() now uses the lesser of n_channels and raw.ch_names, by Joan Massich

• Add support for FIR filtering in mne.io.Raw.plot() and mne browse_raw by passing filtorder=0 or --filtorder 0, respectively, by Eric Larson

• Add chunk_duration parameter to mne.events_from_annotations() to allow multiple events from a single annotation by Joan Massich

• Add mne.simulation.SourceSimulator class to simplify simulating SourceEstimates, by Samuel Deslauriers-Gauthier, Kostiantyn Maksymenko, Nathalie Gayraud, Ivana Kojcic, Alex Gramfort, and Eric Larson

• mne.io.read_raw_edf() now detects analog stim channels labeled 'STATUS' and sets them as stim channel. mne.io.read_raw_edf() no longer synthesize TAL annotations into stim channel but stores them in raw.annotations when reading by Joan Massich

• Add mne.simulation.add_noise for ad-hoc noise addition to io.Raw, Epochs, and Evoked instances, by Eric Larson

• Add drop_refs=True parameter to set_bipolar_reference() to drop/keep anode and cathode channels after applying the reference by Cristóbal Moënne-Loccoz.

• Add processing of reference MEG channels to mne.preprocessing.ICA by Jevri Hanna

• Add use of scipy.signal.windows.dpss() for faster multitaper window computations in PSD functions by Eric Larson

• Add mne.morph_labels() to facilitate morphing label sets obtained from parcellations, by Eric Larson

• Add mne.labels_to_stc() to facilitate working with label data, by Eric Larson

• Add mne.label.select_sources() to simplify the selection of sources within a label, by Samuel Deslauriers-Gauthier

• Add support for using mne.Info in mne.simulation.simulate_raw() instead of mne.io.Raw by Eric Larson

• Add support for passing an iterable and stim channel values using stc parameter of mne.simulation.simulate_raw() by Eric Larson

• Add overlap argument to mne.make_fixed_length_events() by Eric Larson

• Add approximate distance-based spacing source space decimation algorithm to mne.setup_source_space() by Eric Larson

• Add 448-labels subdivided aparc cortical parcellation by Denis Engemann and Sheraz Khan

• Add option to improve rendering in mne coreg for modern graphics cards by Eric Larson

• Add mne.preprocessing.mark_flat to automate marking of flat channels and segments of raw data by Eric Larson

• Add support for CUDA-based correlation computations and progress bars in mne.decoding.ReceptiveField by Eric Larson

• Add support for file-like objects in mne.io.read_raw_fif() as long as preloading is used by Eric Larson

• Add keyboard shortcuts to nativate volume source estimates in time using (shift+)left/right arrow keys by Mainak Jas

• Add option to SSP preprocessing functions (e.g., mne.preprocessing.compute_proj_eog() and mne.compute_proj_epochs()) to process MEG channels jointly with meg='combined' by Eric Larson

• Add Epoch selection and metadata functionality to mne.time_frequency.EpochsTFR using new mixin class by Keith Doelling

• Add reject_by_annotation argument to mne.preprocessing.find_ecg_events() by Eric Larson

• Add pca argument to return the rank-reduced whitener in mne.cov.compute_whitener() by Eric Larson

• Add extrapolate argument to mne.viz.plot_topomap() for better control of extrapolation points placement by Mikołaj Magnuski

• Add channel_wise argument to mne.io.Raw.apply_function() to allow applying a function on multiple channels at once by Hubert Banville

• Add option copy='auto' to control data copying in mne.io.RawArray by Eric Larson

• The mri parameter in mne.setup_volume_source_space() is now automatically set to T1.mgz if subject is provided. This allows to get a mne.SourceSpaces of kind volume more automatically. By Alex Gramfort

• Add better __repr__ for constants, and info['dig'] entries via DigPoint by Eric Larson

• Allow string argument in mne.io.Raw.drop_channels() to remove a single channel by Clemens Brunner

• Add additional depth weighting options for inverse solvers (e.g., mne.inverse_sparse.gamma_map() and mne.inverse_sparse.mixed_norm()) by Eric Larson

• Add depth weighting to LCMV beamformers via depth argument in mne.beamformer.make_lcmv() by Eric Larson

• Allow toggling of DC removal in mne.io.Raw.plot() by pressing the ‘d’ key by Clemens Brunner

• Improved clicking in mne.io.Raw.plot() (left click on trace toggles bad, left click on background sets green line, right click anywhere removes green line) by Clemens Brunner

• Add mne.realtime.LSLClient for realtime data acquisition with LSL streams of data by Teon Brooks and Mainak Jas

• Add partial support for PyVista as a 3D backend using mne.viz.use_3d_backend() by Guillaume Favelier

• Add option ids = None in mne.event.shift_time_events() for considering all events by Nikolas Chalas and Joan Massich

• Add mne.realtime.MockLSLStream to simulate an LSL stream for testing and examples by Teon Brooks

• Add support for file-like objects in mne.read_epochs() as long as preloading is used by Paul Roujansky

Bug

• Fix annotations in split fif files mne.io.read_raw_fif() by Joan Massich

• Fix mne.Epochs.plot() with scalings='auto' to properly compute channel-wise scalings by Stefan Repplinger

• Fix mne.gui.coregistration() and mne coreg crashing with segmentation fault when switching subjects by Eric Larson

• Fix mne.io.read_raw_brainvision() to accommodate vmrk files which do not have any annotations by Alexander Kovrig

• Fix mne.io.Raw.plot() and mne.Epochs.plot() to auto-scale misc channel types by default by Eric Larson

• Fix filtering functions (e.g., mne.io.Raw.filter()) to properly take into account the two elements in n_pad parameter by Bruno Nicenboim

• Fix feature_names parameter change after fitting in mne.decoding.ReceptiveField by Jean-Remi King

• Fix index error in mne.io.read_raw_cnt() when creating stim_channel manually by Joan Massich

• Fix bug with weight_norm='unit-gain' in mne.beamformer.make_lcmv() and mne.beamformer.make_dics() by Britta Westner

• Fix 32bits annotations in mne.io.read_raw_cnt() by Joan Massich

• Fix mne.events_from_annotations() to ignore 'BAD_'` and ``'EDGE_' annotations by default using a new default regexp by Eric Larson

• Fix bug in mne.preprocessing.mark_flat where raw.first_samp was not taken into account by kalenkovich

• Fix date parsing in mne.io.read_raw_cnt() by Joan Massich

• Fix topological checks and error messages for BEM surfaces in mne.make_bem_model() by Eric Larson

• Fix default HTML language of mne.Report to be "en-us" instead of "fr" and allow setting via report.lang property by Eric Larson

• Fix bug where loading epochs with preload=True and subsequently using mne.Epochs.drop_bad() with new reject or flat entries leads to improper data (and epochs.selection) since v0.16.0 by Eric Larson. If your code uses Epochs(..., preload=True).drop_bad(reject=..., flat=...), we recommend regenerating these data.

• Fix mne flash_bem to properly utilize flash30 images when conversion from DICOM images is used, and to properly deal with non-standard acquisition affines by Eric Larson

• Fix mne.io.Raw.set_annotations() with annotations=None to create an empty annotations object with orig_time that matches the mne.io.Raw instance by Eric Larson

• Fix mne.io.read_raw_edf() returning all the annotations with the same name in GDF files by Joan Massich

• Fix boundaries during plotting of raw data with mne.io.Raw.plot() and mne browse_raw on scaled displays (e.g., macOS with HiDPI/Retina screens) by Clemens Brunner

• Fix bug where filtering was not performed with lowpass or highpass in mne.io.Raw.plot() and mne browse_raw by Eric Larson

• Fix mne.simulation.simulate_evoked() that was failing to simulate the noise with heterogeneous sensor types due to poor conditioning of the noise covariance and make sure the projections from the noise covariance are taken into account Alex Gramfort

• Fix checking of data dimensionality in mne.SourceEstimate and related constructors by Eric Larson

• Fix mne.io.Raw.append() annotations miss-alignment by Joan Massich

• Fix hash bug in the mne.io.edf module when installing on Windows by Eric Larson

• Fix mne.io.read_raw_edf() reading duplicate channel names by Larry Eisenman

• Fix set_bipolar_reference() in the case of generating all bipolar combinations and also in the case of repeated channels in both lists (anode and cathode) by Cristóbal Moënne-Loccoz

• Fix missing code for computing the median when method='median' in mne.Epochs.average() by Cristóbal Moënne-Loccoz

• Fix CTF helmet plotting in mne.viz.plot_evoked_field() by Eric Larson

• Fix saving of rejection parameters in mne.Epochs.save() by Eric Larson

• Fix orientations returned by mne.dipole.get_phantom_dipoles() (half were flipped 180 degrees) by Eric Larson

• Fix bug in mne.viz.plot_compare_evokeds() when evoked.times[0] >= 0 would cause a problem with vlines='auto' mode by Eric Larson

• Fix path bugs in mne.bem.make_flash_bem() and mne flash_bem by Eric Larson

• Fix mne.time_frequency.AverageTFR.plot_joint() mishandling bad channels, by David Haslacher and Jona Sassenhagen

• Fix mne.beamformer.make_lcmv() failing when full rank data is used (i.e., when no projection is done) with reg=0., by Eric Larson

• Fix issue with bad channels ignored in mne.beamformer.make_lcmv() and mne.beamformer.make_dics() by Alex Gramfort

• Fix mne.compute_proj_raw() when duration != None not to apply existing proj and to avoid using duplicate raw data samples by Eric Larson

• Fix reject_by_annotation not being passed internally by mne.preprocessing.create_ecg_epochs() and mne clean_eog_ecg to mne.preprocessing.find_ecg_events() by Eric Larson

• Fix mne.io.read_raw_edf() failing when EDF header fields (such as patient name) contained special characters, by Clemens Brunner

• Fix mne.io.read_raw_eeglab() incorrectly parsing event durations by Clemens Brunner

• Fix mne.io.read_raw_egi() when cropping non-preloaded EGI MFF data by Alex Gramfort

• Fix mne.io.Raw.interpolate_bads() for interpolating CTF MEG channels when reference sensors are present by jeythekey

• Fix a bug in mne.io.Raw.resample(), where resampling events could result in indices > n_times-1, by jeythekey

• Fix mne.preprocessing.ICA.score_sources() to use the sfreq of the raw data to filter rather than the sfreq when the ICA was fit, by jeythekey

• Fix a bug in mne.preprocessing.ICA, where manually setting the attribute ICA.exclude to an np.array resulted in the removal of random components when later also providing the exclude argument to any apply...-method, by jeythekey

• Ascending changed to descending sorting of scores for integer ..._criterion arguments in mne.preprocessing.ICA.detect_artifacts and mne.preprocessing.run_ica, as it used to be documented; the docstring in these functions was corrected for float ..._criterion arguments, by jeythekey

API

• Deprecate cov, iir_params, blink, ecg, chpi, random_state and support for mne.io.Raw instance inputs in mne.simulation.simulate_raw(); use mne.simulation.add_noise(), mne.simulation.add_ecg(), mne.simulation.add_eog(), and mne.simulation.add_chpi() by Eric Larson

• Add overwrite parameter in mne.Epochs.save() by Katarina Slama

• Add stim_channel parameter in mne.io.read_raw_cnt() to toggle stim channel synthesis by Joan Massich

• Python 2 is no longer supported; MNE-Python now requires Python 3.5+, by Eric Larson

• A new class mne.VolVectorSourceEstimate is returned by mne.minimum_norm.apply_inverse() (and related functions) when a volume source space and pick_ori='vector' is used, by Eric Larson

• Converting a forward solution with a volume source space to fixed orientation using mne.convert_forward_solution() now raises an error, by Eric Larson

• raw.estimate_rank has been deprecated and will be removed in 0.19 in favor of mne.compute_rank() by Eric Larson

• Annotations are now kept sorted (by onset time) during instantiation and append() operations, by Eric Larson

• Deprecate mne.io.find_edf_events by Joan Massich

• Deprecate limit_depth_chs in mne.minimum_norm.make_inverse_operator() in favor of depth=dict(limit_depth_chs=...) by Eric Larson

• Reading BDF and GDF files with mne.io.read_raw_edf() is deprecated and replaced by mne.io.read_raw_bdf() and mne.io.read_raw_gdf(), by Clemens Brunner

• mne.forward.compute_depth_prior() has been reworked to operate directly on Forward instance as forward rather than a representation scattered across the parameters G, is_fixed_ori, patch_info, by Eric Larson

• Deprecate method='extended-infomax' in mne.preprocessing.ICA; Extended Infomax can now be computed with method='infomax' and fit_params=dict(extended=True) by Clemens Brunner

• Fix support for supplying extrapolate via ica.plot_properties(..., topomap_args=dict(extrapolate=...)) by Sebastian Castano

• The peak finder that was formerly accessible via from mne.preprocessing.peak_finder import peak_finder should now be imported directly from the enclosing namespace as from mne.preprocessing import peak_finder by Eric Larson

• Deprecate mne.realtime module to make a standalone module mne-realtime that will live outside of this package by Teon Brooks

Version 0.17 (2018-11-19)

Changelog

• Add new tutorial for mne.Annotations and events by Joan Massich and Alex Gramfort

• Add support for saving mne.Annotations as CSV and TXT files by Joan Massich and Alex Gramfort

• Add mne.Epochs.shift_time() that shifts the time axis of mne.Epochs by Thomas Hartmann

• Add mne.viz.plot_arrowmap() computes arrowmaps using Hosaka-Cohen transformation from magnetometer or gradiometer data, these arrows represents an estimation of the current flow underneath the MEG sensors by Sheraz Khan

• Add mne.io.read_raw_fieldtrip(), mne.read_epochs_fieldtrip() and mne.read_evoked_fieldtrip() to import FieldTrip data. By Thomas Hartmann and Dirk Gütlin.

• Add rank parameter to mne.compute_covariance(), mne.cov.regularize() and related functions to preserve data rank and speed up computation using low-rank computations during regularization by Eric Larson and Denis Engemann

• Add new function mne.read_annotations() that can read annotations in EEGLAB, BrainVision, EDF and Brainstorm formats by Joan Massich and Alex Gramfort.

• Add capability to read and save Epochs containing complex data (e.g. after Hilbert-transform) using mne.Epochs.save() and mne.read_epochs(), by Stefan Repplinger, Eric Larson and Alex Gramfort

• Add optically pumped magnetometer dataset and example by Rasmus Zetter and Eric Larson

• Add orgin parameter to mne.io.Raw.time_as_index() to allow times to be relative to this origin by Joan Massich

• Add title argument to mne.SourceEstimate.plot() by Eric Larson

• mne.io.Raw.set_annotations() now changes orig_time to match meas_date and shift self.annotations.onset accordingly. Previous behavior is deprecated and would be removed in 0.18. Work by Joan Massich

• Add mne.compute_source_morph() which creates a mne.SourceMorph object to unify morphing any type of source estimates (surface or volume) from one subject to another for group studies. It is now possible to do group studies when working on the volume with MNE. Work by Tommy Clausner during GSOC 2018 with the help of Alex Gramfort and Eric Larson.

• Add ability to pass threshold for EOG to mne.preprocessing.find_eog_events() and mne.preprocessing.create_eog_epochs() by Peter Molfese

• Add possibility to save mne.VolSourceEstimate and mne.MixedSourceEstimate to HDF5 format (file extension .h5) with mne.VolSourceEstimate.save() and mne.MixedSourceEstimate.save() by Alex Gramfort

• Add replace parameter to mne.io.Raw.add_events() to allow adding events while removing the old ones on the stim channel by Alex Gramfort

• Add ability to pass axes to ts_args and topomap_args of mne.viz.plot_evoked_joint() by Jona Sassenhagen

• Add ability to pass a precomputed forward solution to mne.simulation.simulate_raw() by Eric Larson

• Add ability to read and write beamformers with mne.beamformer.read_beamformer() and mne.beamformer.Beamformer.save by Eric Larson

• Add resting-state source power spectral estimation example sphx_glr_auto_examples_datasets_plot_opm_rest_data.py by Eric Larson, Denis Engemann, and Luke Bloy

• Add mne.channels.make_1020_channel_selections() to group 10/20-named EEG channels by location, by Jona Sassenhagen

• Add helmet for Artemis123 for mne.viz.plot_alignment() by Eric Larson

• Add support for reading MATLAB v7.3+ files in mne.io.read_raw_eeglab() and mne.read_epochs_eeglab() via pymatreader by Steven Gutstein, Eric Larson, and Thomas Hartmann

• Add support for raw PSD plots in mne.Report.parse_folder() via raw_psd argument of mne.Report by Eric Larson

• Add trig_shift_by_type parameter in mne.io.read_raw_brainvision() to allow to specify offsets for arbitrary marker types by Henrich Kolkhorst

• Add progress bar support to mne.decoding.SlidingEstimator and mne.decoding.GeneralizingEstimator by Eric Larson

• Add interactive visualization of volume source estimates using mne.viz.plot_volume_source_estimates() by Mainak Jas

• Add mne.head_to_mri() to convert positions from head coordinates to MRI RAS coordinates, by Joan Massich and Alex Gramfort

• Add improved CTF helmet for mne.viz.plot_alignment() by Eric Larson

• Add handling in mne.combine_evoked() and mne.grand_average() for input with the same channels in different orders, if required, by Jona Sassenhagen

• Add split_naming parameter to the mne.io.Raw.save method to allow for BIDS-compatible raw file name construction by Teon Brooks

• Add origin parameter to mne.Evoked.interpolate_bads() and related methods by Eric Larson

• Add automated MEG helmet shape approximation to mne.viz.plot_alignment() by Eric Larson

• Add capability to save a mne.Report to an HDF5 file to mne.Report.save() by Marijn van Vliet

• Add mne.open_report() to read back a mne.Report object that was saved to an HDF5 file by Marijn van Vliet

• Add multi-taper estimation to mne.minimum_norm.compute_source_psd() by Eric Larson

• Add support for custom, e.g. robust, averaging methods in mne.Epochs.average() by Jona Sassenhagen

• Add support for Neuromag 122 system by Alex Gramfort

• Add function mne.io.read_annotations_brainvision for reading directly Brainvision marker files by Alex Gramfort

• Add mne.Report.remove() method to remove existing figures from a report, by Marijn van Vliet

• Add sign to output of max-power orientation for mne.beamformer.make_dics() by Eric Larson

• Add support for pick_ori='max-power' when weight_norm=None in mne.beamformer.make_lcmv() by Marijn van Vliet

• Add support for weight_norm='nai' for all pick_ori options in mne.beamformer.make_lcmv() by Marijn van Vliet

• Add support for weight_norm='nai' to mne.beamformer.make_dics() by Marijn van Vliet

• Add parameter rank=None to mne.beamformer.make_dics() by Marijn van Vliet

• Add parameter rank='full' to mne.beamformer.make_lcmv(), which can be set to None to auto-compute the rank of the covariance matrix before regularization by Marijn van Vliet

• Handle different time vectors in topography plots using mne.viz.plot_evoked_topo() by Jussi Nurminen

• Speed up mne.inverse_sparse.mixed_norm() if the solver parameter is set to bcd using scipy.linalg.get_blas_funcs() by Quentin Bertrand

Bug

• Fix bug with scaling of data in mne.cov._compute_covariance_auto that was affecting the mne.decoding.SPoC estimator by David Sabbagh

• Fix mne.io.Raw.plot_projs_topomap() by Joan Massich

• Fix bug in mne.minimum_norm.compute_source_psd() where the stc.times output was scaled by 1000, by Eric Larson

• Fix default values for 'diagonal_fixed' estimation method of mne.compute_covariance() to be 0.1 for all channel types, as in mne.cov.regularize() by Eric Larson

• Fix reading edf file annotations by Joan Massich

• Fix bug with reading events from BrainVision files by Stefan Appelhoff

• Fix bug where mne.io.read_raw_eeglab() would warn when the stim channel is populated with an array of zeros by Joan Massich

• Fix 2nd column of events in BrainVision to no longer store duration but rather be contained by raw.annotations by Alex Gramfort

• Fix checking of the correctness of the prepared=True argument in mne.minimum_norm.apply_inverse() and related functions by Eric Larson

• Fix bug of not showing ERD’s in baseline rescaled tfr topomaps if grads are combined by Erkka Heinila

• Fix bug with FIF I/O where strings were written in UTF-8 format instead of Latin-1 by Eric Larson

• Fix bug with reading measurement dates from BrainVision files by Stefan Appelhoff

• Fix bug with mne.fit_dipole where the residual was returned as ndarray instead of mne.Evoked instance, by Eric Larson

• Fix bug with mne flash_bem when flash30 is not used by Eric Larson

• Fix bug with mne.stats.permutation_cluster_test() and mne.stats.spatio_temporal_cluster_test() where threshold=None was not calculated properly for a f-oneway test by Daniel McCloy and Eric Larson

• Fix bug with channel names in mgh70 montage in mne.channels.read_montage by Eric Larson

• Fix duplication of info['hpi_meas'] and info['hpi_results'] by Sara Sommariva

• Fix bug in mne.io.read_raw_edf() when reading large files on Windows by Marcin Koculak

• Fix check in mne.viz.plot_sensors() for invalid channel locations by Eric Larson

• Fix bug in mne.io.read_raw_edf() where GDF files had info['highpass'] and info['lowpass'] set to NaN and info['meas_date'] set incorrectly, by Eric Larson

• Fix bug in mne.preprocessing.ICA.apply() to handle arrays as exclude property by Joan Massich

• Fix bug in method='eLORETA' for mne.minimum_norm.apply_inverse() when using a sphere model and saved inv by Eric Larson

• Fix bug in mne.io.Raw where warnings were emitted when objects were deleted by Eric Larson

• Fix vector data support for mne.VolSourceEstimate by Christian Brodbeck

• Fix bug with IIR filtering axis in mne.filter.filter_data() by Eric Larson

• Fix bug with non-boxcar windows in mne.io.Raw.resample() and mne.filter.resample() by Eric Larson

• Fix bug in mne.minimum_norm.apply_inverse() where applying an MEG-only inverse would raise an error about needing an average EEG reference by Eric Larson

• Fix bug in inst.apply_proj() where an average EEG reference was always added by Eric Larson

• Fix bug in mne.time_frequency.tfr_morlet(), mne.time_frequency.tfr_multitaper(), and mne.time_frequency.tfr_stockwell() where not all data channels were picked by Eric Larson

• Fix bug in mne.preprocessing.ICA.plot_overlay() and mne.make_field_map() for CTF data with compensation by Eric Larson

• Fix bug in mne.create_info() passing int as ch_names on Windows by Eric Larson

• Fix bug in mne.realtime.RtEpochs where events during the buildup of the buffer were not correctly processed when incoming data buffers are smaller than the epochs by Henrich Kolkhorst

• Fix bug in mne.io.read_raw_brainvision() where 1-indexed BrainVision events were not being converted into 0-indexed mne events by Steven Bethard

• Fix bug in mne.viz.plot_snr_estimate() and mne.minimum_norm.estimate_snr() where the inverse rank was not properly utilized (especially affecting SSS’ed MEG data) by Eric Larson

• Fix error when saving stc as nifti image when using volume source space formed by more than one label by Alex Gramfort

• Fix error when interpolating MEG channels with compensation using reference channels (like for CTF data) by Alex Gramfort

• Fix bug in mne.make_sphere_model() where EEG sphere model coefficients were not optimized properly by Eric Larson

• Fix bug in mne.io.read_raw_ctf() to read bad channels and segments from CTF ds files by Luke Bloy

• Fix problem with mne.io.Raw.add_channels() where raw.info['bads'] was replicated by Eric Larson

• Fix bug with mne.Epochs where an error was thrown when resizing data (e.g., during mne.Epochs.drop_bad()) by Eric Larson

• Fix naming of raw.info['buffer_size_sec'] to be raw.buffer_size_sec as it is a writing parameter rather than a measurement parameter by Eric Larson

• Fix EGI-MFF parser not to require dateutil package by Eric Larson

• Fix error when running LCMV on MEG channels with compensation using reference channels (like for CTF data) by Alex Gramfort

• Fix the use of sklearn.model_selection.cross_val_predict() with mne.decoding.SlidingEstimator by Alex Gramfort

• Fix event sample number increase when combining many Epochs objects with mne.concatenate_epochs() with by Jasper van den Bosch

• Fix title of custom slider images to mne.Report by Marijn van Vliet

• Fix missing initialization of self._current in mne.Epochs by Henrich Kolkhorst

• Fix processing of data with bad segments and acquisition skips with new skip_by_annotation parameter in mne.preprocessing.maxwell_filter() by Eric Larson

• Fix symlinking to use relative paths in mne flash_bem` and ``mne watershed_bem by Eric Larson

• Fix error in mne coreg when saving with scaled MRI if fiducials haven’t been saved by Ezequiel Mikulan

• Fix normalization error in mne.beamformer.make_lcmv() when pick_ori='normal', weight_norm='unit_noise_gain' by Marijn van Vliet

• Fix MNE-C installation instructions by buildqa

• Fix computation of max-power orientation in mne.beamformer.make_dics() when pick_ori='max-power', weight_norm='unit_noise_gain' by Marijn van Vliet

API

• Deprecated separate reading of annotations and synthesis of STI014 channels in readers by Joan Massich:

  • Deprecated mne.io.read_annotations_eeglab

  • Deprecated annot and annotmap parameters in read_raw_edf()

  • Deprecated stim_channel parameters in read_raw_edf(), read_raw_brainvision(), and read_raw_eeglab()

  Annotations are now added to raw instances directly upon reading as raw.annotations. They can also be read separately with mne.read_annotations() for EEGLAB, BrainVision, EDF, and Brainstorm formats. Use mne.events_from_annotations(raw.annotations) to convert these to events instead of the old way (using STI014 channel synthesis followed by mne.find_events(raw)).

  In 0.17 (this release)

  Use read_raw_...(stim_channel=False) to disable warnings (and stim channel synthesis), but other arguments for stim_channel will still be supported.

  In 0.18

  The only supported option will be read_raw_...(stim_channel=False), and all stim-channel-synthesis arguments will be removed. At this point, stim_channel should be removed from scripts for future compatibility, but stim_channel=False will still be acceptable for backward compatibility.

  In 0.19

  The stim_channel keyword arguments will be removed from read_raw_... functions.

• Calling :meth:mne.io.pick.pick_info removing channels that are needed by compensation matrices (info['comps']) no longer raises RuntimeException but instead logs an info level message. By Luke Bloy

• mne.Epochs.save() now has the parameter fmt to specify the desired format (precision) saving epoched data, by Stefan Repplinger, Eric Larson and Alex Gramfort

• Deprecated mne.SourceEstimate.morph_precomputed, mne.SourceEstimate.morph, mne.compute_morph_matrix, mne.morph_data_precomputed and mne.morph_data in favor of mne.compute_source_morph(), by Tommy Clausner

• Prepare transition to Python 3. This release will be the last release compatible with Python 2. The next version will be Python 3 only.

• CUDA support now relies on CuPy instead of PyCUDA and scikits-cuda. It can be installed using conda install cupy. By Eric Larson

• Functions requiring a color cycle will now default to Matplotlib rcParams colors, by Stefan Appelhoff

• mne.Evoked.plot_image() has gained the ability to show_names, and if a selection is provided to group_by, axes can now receive a dict, by Jona Sassenhagen

• Calling mne.Epochs.decimate() with decim=1 no longer copies the data by Henrich Kolkhorst

• Removed blocking (waiting for new epochs) in mne.realtime.RtEpochs.get_data() by Henrich Kolkhorst

• Warning messages are now only emitted as warnings.warn_explicit() rather than also being emitted as logging messages (unless a logging file is being used) to avoid duplicate warning messages, by Eric Larson

• Deprecated save_stc_as_volume function in favor of mne.VolSourceEstimate.as_volume() and mne.VolSourceEstimate.save_as_volume() by Alex Gramfort

• src.kind now equals to 'mixed' (and not 'combined') for a mixed source space (made of surfaces and volume grids) by Alex Gramfort

• Deprecation of mne.io.Raw.annotations property in favor of mne.io.Raw.set_annotations() by Joan Massich

• The default value of stop_receive_thread in mne.realtime.RtEpochs.stop has been changed to True by Henrich Kolkhorst

• Using the mne.io.Raw.add_channels() on an instance with memmapped data will now resize the memmap file to append the new channels on Windows and Linux, by Eric Larson

• mne.io.Raw.annotations when missing is set to an empty mne.Annotations rather than None by Joan Massich and Alex Gramfort

• Mismatches in CTF compensation grade are now checked in inverse computation by Eric Larson

Authors

People who contributed to this release (in alphabetical order):

• Alexandre Gramfort

• Antoine Gauthier

• Britta Westner

• Christian Brodbeck

• Clemens Brunner

• Daniel McCloy

• David Sabbagh

• Denis A. Engemann

• Eric Larson

• Ezequiel Mikulan

• Henrich Kolkhorst

• Hubert Banville

• Jasper J.F. van den Bosch

• Jen Evans

• Joan Massich

• Johan van der Meer

• Jona Sassenhagen

• Kambiz Tavabi

• Lorenz Esch

• Luke Bloy

• Mainak Jas

• Manu Sutela

• Marcin Koculak

• Marijn van Vliet

• Mikolaj Magnuski

• Peter J. Molfese

• Sam Perry

• Sara Sommariva

• Sergey Antopolskiy

• Sheraz Khan

• Stefan Appelhoff

• Stefan Repplinger

• Steven Bethard

• Teekuningas

• Teon Brooks

• Thomas Hartmann

• Thomas Jochmann

• Tom Dupré la Tour

• Tristan Stenner

• buildqa

• jeythekey

Version 0.16 (2018-05-01)

Changelog

• Add possibility to pass dict of floats as argument to mne.make_ad_hoc_cov() by Nathalie Gayraud

• Add support for metadata in mne.Epochs by Chris Holdgraf, Alex Gramfort, Jona Sassenhagen, and Eric Larson

• Add support for plotting a dense head in mne.viz.plot_alignment() by Eric Larson

• Allow plotting in user-created mayavi Scene in mne.viz.plot_alignment() by Daniel McCloy

• Reduce memory consumption and do not require data to be loaded in mne.Epochs.apply_baseline() by Eric Larson

• Add option render_bem to mne.Report.parse_folder() by Eric Larson

• Add to mne.viz.plot_alignment() plotting of coordinate frame axes via show_axes and terrain-style interaction via interaction, by Eric Larson

• Add option initial_event to mne.find_events() by Clemens Brunner

• Left and right arrow keys now scroll by 25% of the visible data, whereas Shift+left/right scroll by a whole page in mne.io.Raw.plot() by Clemens Brunner

• Add support for gantry tilt angle determination from Elekta FIF file header by Chris Bailey

• Add possibility to concatenate mne.Annotations objects with + or += operators by Clemens Brunner

• Add support for MaxShield raw files in mne.Report by Eric Larson

• Add ability to plot whitened data in mne.io.Raw.plot(), mne.Epochs.plot(), mne.Evoked.plot(), and mne.Evoked.plot_topo() by Eric Larson

• Workaround for reading EGI MFF files with physiological signals that also present a bug from the EGI system in mne.io.read_raw_egi() by Federico Raimondo

• Add support for reading subject height and weight in info['subject_info'] by Eric Larson

• Improve online filtering of raw data when plotting with mne.io.Raw.plot() to filter in segments in accordance with the default skip_by_annotation=('edge', 'bad_acq_skip') of mne.io.Raw.filter() to avoid edge ringing by Eric Larson

• Add support for multiple head position files, plotting of sensors, and control of plotting color and axes in mne.viz.plot_head_positions() by Eric Larson

• Add ability to read and write Annotations separate from mne.io.Raw instances via Annotations.save() and read_annotations() by Eric Larson

• Add option to unset a montage by passing None to mne.io.Raw.set_montage() by Clemens Brunner

• Add sensor denoising via mne.preprocessing.oversampled_temporal_projection() by Eric Larson

• Add mne.io.pick.get_channel_types which returns all available channel types in MNE by Clemens Brunner

• Use standard PCA instead of randomized PCA whitening prior to ICA to increase reproducibility by Clemens Brunner

• Plot sEEG electrodes in mne.viz.plot_alignment() by Alex Gramfort

• Add support for any data type like sEEG or ECoG in covariance related functions (estimation, whitening and plotting) by Alex Gramfort and Eric Larson

• Add function mne.io.read_annotations_eeglab to allow loading annotations from EEGLAB files, by Alex Gramfort

• mne.io.Raw.set_montage() now accepts a string as its montage argument; this will set a builtin montage, by Clemens Brunner

• Add 4D BTi phantom dataset mne.datasets.phantom_4dbti.data_path(), by Alex Gramfort

• Changed the background color to grey in mne.viz.plot_alignment() to make helmet more visible, by Alex Gramfort

• Add mne.io.Raw.reorder_channels(), mne.Evoked.reorder_channels(), etc. to reorder channels, by Eric Larson

• Add to mne coreg and mne.gui.coregistration() by Eric Larson:

  • Improved visibility of points inside the head

  • Projection of EEG electrodes

  • Orientation of extra points toward the surface

  • Scaling points by distance to the head surface

  • Display of HPI points

  • ICP fitting with convergence criteria

  • Faster display updates

  • Scaling of mri/*.mgz files

  • Scaling of mri/trainsforms/talairach.xfm files for conversion to MNI space

• Add ability to exclude components interactively by clicking on their labels in mne.preprocessing.ICA.plot_components() by Mikołaj Magnuski

• Add reader for manual annotations of raw data produced by Brainstorm by Anne-Sophie Dubarry

• Add eLORETA noise normalization for minimum-norm solvers by Eric Larson

• Tighter duality gap computation in mne.inverse_sparse.tf_mxne_optim and new parametrization with alpha and l1_ratio instead of alpha_space and alpha_time by Mathurin Massias and Daniel Strohmeier

• Add dgap_freq parameter in mne.inverse_sparse.mxne_optim solvers to control the frequency of duality gap computation by Mathurin Massias and Daniel Strohmeier

• Add support for reading Eximia files by Eric Larson and Federico Raimondo

• Add the Picard algorithm to perform ICA for mne.preprocessing.ICA, by Pierre Ablin and Alex Gramfort

• Add ability to supply a mask to the plot in mne.viz.plot_evoked_image() by Jona Sassenhagen

• Add connectivity=False to cluster-based statistical functions to perform non-clustering stats by Eric Larson

• Add mne.time_frequency.csd_morlet() and mne.time_frequency.csd_array_morlet() to estimate cross-spectral density using Morlet wavelets, by Marijn van Vliet

• Add multidictionary time-frequency support to mne.inverse_sparse.tf_mixed_norm() by Mathurin Massias and Daniel Strohmeier

• Add new DICS implementation as mne.beamformer.make_dics(), mne.beamformer.apply_dics(), mne.beamformer.apply_dics_csd() and mne.beamformer.apply_dics_epochs(), by Marijn van Vliet and Susanna Aro

Bug

• Fix bug in EEG interpolation code to do nothing if there is no channel to interpolate by Mainak Jas

• Fix bug in mne.preprocessing.peak_finder to output datatype consistently and added input check for empty vectors by Tommy Clausner

• Fix bug in mne.io.read_raw_brainvision() to use the correct conversion for filters from time constant to frequency by Stefan Appelhoff

• Fix bug with events when saving split files using mne.Epochs.save() by Eric Larson

• Fix bug in mne.decoding.SlidingEstimator and mne.decoding.GeneralizingEstimator to allow mne.decoding.cross_val_multiscore() to automatically detect whether the base_estimator is a classifier and use a StratifiedKFold instead of a KFold when cv is not specified, by Jean-Remi King

• Fix bug in mne.set_eeg_reference() to remove an average reference projector when setting the reference to [] (i.e. do not change the existing reference) by Clemens Brunner

• Fix bug in threshold-free cluster enhancement parameter validation (mne.stats.permutation_cluster_1samp_test() and mne.stats.permutation_cluster_test()) by Clemens Brunner

• Fix bug in mne.io.Raw.plot() to correctly display event types when annotations are present by Clemens Brunner

• Fix bug in mne.stats.spatio_temporal_cluster_test() default value for threshold is now calculated based on the array sizes in X, by Eric Larson

• Fix bug in mne.simulation.simulate_raw() with use_cps=True where CPS was not actually used by Eric Larson

• Fix bug in mne.simulation.simulate_raw() where 1- and 3-layer BEMs were not properly transformed using trans by Eric Larson

• Fix bug in mne.viz.plot_alignment() where the head surface file -head.fif was not used even though present by Chris Bailey

• Fix bug when writing compressed sparse column matrices (e.g., Maxwell filtering cross-talk matrices) by Marijn van Vliet and Eric Larson

• Fix bug in mne.io.Raw.plot_psd() to correctly deal with reject_by_annotation=False by Clemens Brunner

• Fix bug in mne.make_fixed_length_events() when hitting corner case problems rounding to sample numbers by Eric Larson

• Fix bug in mne.Epochs when passing events as list with event_id=None by Alex Gramfort

• Fix bug in mne.Report.add_figs_to_section when passing numpy.ndarray by Eric Larson

• Fix bug in CSS class setting in mne.Report BEM section by Eric Larson

• Fix bug in Annotations where annotations that extend to the end of a recording were not extended properly by Eric Larson

• Fix bug in mne.io.Raw.filter() to properly raw data with acquisition skips in separate segments by Eric Larson

• Fix bug in mne.preprocessing.maxwell_filter() where homogeneous fields were not removed for CTF systems by Eric Larson

• Fix computation of average quaternions in mne.preprocessing.maxwell_filter() by Eric Larson

• Fix bug in writing raw.annotations where empty annotations could not be written to disk, by Eric Larson

• Fix support for writing FIF files with acquisition skips by using empty buffers rather than writing zeros by Eric Larson

• Fix bug in the mne make_scalp_surfaces command where --force (to bypass topology check failures) was ignored by Eric Larson

• Fix bug in mne.preprocessing.maxwell_filter() when providing origin in 'meg' coordinate frame for recordings with a MEG to head transform (i.e., non empty-room recordings) by Eric Larson

• Fix bug in mne.viz.plot_cov() that ignored colorbar argument by Nathalie Gayraud

• Fix bug when picking CTF channels that could cause data saved to disk to be unreadable by Eric Larson

• Fix bug when reading event latencies (in samples) from eeglab files didn’t translate indices to 0-based python indexing by Mikołaj Magnuski

• Fix consistency between mne.Epochs and mne.stats.linear_regression_raw() in converting between samples and times (mne.stats.linear_regression_raw() now rounds, instead of truncating) by Phillip Alday

• Fix bug in mne coreg where sphere surfaces were scaled by Eric Larson

• Fix bug in mne.Evoked.plot_topomap() when using proj='interactive' mode by Eric Larson

• Fix bug when passing show_sensors=1 to mne.viz.plot_compare_evokeds() resulted in sensors legend placed in lower right of the figure (position 4 in matplotlib), not upper right by Mikołaj Magnuski

• Fix handling of annotations when cropping and concatenating raw data by Alex Gramfort and Eric Larson

• Fix bug in mne.preprocessing.create_ecg_epochs() where keep_ecg=False was ignored by Eric Larson

• Fix bug in mne.io.Raw.plot_psd() when picks is not None and picks spans more than one channel type by Eric Larson

• Fix bug in mne.make_forward_solution when passing data with compensation channels (e.g. CTF) that contain bad channels by Alex Gramfort

• Fix bug in mne.SourceEstimate.get_peak() and mne.VolSourceEstimate.get_peak() when there is only a single time point by Marijn van Vliet

• Fix bug in mne.io.read_raw_edf() when reading BDF files stimulus channels are now not scaled anymore by Clemens Brunner

API

• Channels with unknown locations are now assigned position [np.nan, np.nan, np.nan] instead of [0., 0., 0.], by Eric Larson

• Removed unused image_mask argument from mne.viz.plot_topomap() by Eric Larson

• Unknown measurement dates are now stored as info['meas_date'] = None rather than using the current date. None is also now used when anonymizing data and when determining the machine ID for writing files, by Mainak Jas and Eric Larson

• mne.Evoked.plot() will now append the number of epochs averaged for the evoked data in the first plot title, by Eric Larson

• Changed the line width in mne.viz.plot_bem() from 2.0 to 1.0 for better visibility of underlying structures, by Eric Larson

• Changed the behavior of mne.io.Raw.pick_channels() and similar methods to be consistent with mne.pick_channels() to treat channel list as a set (ignoring order) – if reordering is necessary use inst.reorder_channels, by Eric Larson

• Changed the labeling of some plotting functions to use more standard capitalization and units, e.g. “Time (s)” instead of “time [sec]” by Eric Larson

• mne.time_frequency.csd_epochs has been refactored into mne.time_frequency.csd_fourier() and mne.time_frequency.csd_multitaper(), by Marijn van Vliet

• mne.time_frequency.csd_array has been refactored into mne.time_frequency.csd_array_fourier() and mne.time_frequency.csd_array_multitaper(), by Marijn van Vliet

• Added clean_names=False parameter to mne.io.read_raw_ctf() for control over cleaning of main channel names and compensation channel names from CTF suffixes by Oleh Kozynets

• The functions lcmv, lcmv_epochs, and lcmv_raw are now deprecated in favor of mne.beamformer.make_lcmv() and mne.beamformer.apply_lcmv(), mne.beamformer.apply_lcmv_epochs(), and mne.beamformer.apply_lcmv_raw(), by Britta Westner

• The functions mne.beamformer.dics, mne.beamformer.dics_epochs and mne.beamformer.dics_source_power are now deprecated in favor of mne.beamformer.make_dics(), mne.beamformer.apply_dics(), and mne.beamformer.apply_dics_csd(), by Marijn van Vliet

Authors

People who contributed to this release (in alphabetical order):

• Alejandro Weinstein

• Alexandre Gramfort

• Annalisa Pascarella

• Anne-Sophie Dubarry

• Britta Westner

• Chris Bailey

• Chris Holdgraf

• Christian Brodbeck

• Claire Braboszcz

• Clemens Brunner

• Daniel McCloy

• Denis A. Engemann

• Desislava Petkova

• Dominik Krzemiński

• Eric Larson

• Erik Hornberger

• Fede Raimondo

• Henrich Kolkhorst

• Jean-Remi King

• Jen Evans

• Joan Massich

• Jon Houck

• Jona Sassenhagen

• Juergen Dammers

• Jussi Nurminen

• Kambiz Tavabi

• Katrin Leinweber

• Kostiantyn Maksymenko

• Larry Eisenman

• Luke Bloy

• Mainak Jas

• Marijn van Vliet

• Mathurin Massias

• Mikolaj Magnuski

• Nathalie Gayraud

• Oleh Kozynets

• Phillip Alday

• Pierre Ablin

• Stefan Appelhoff

• Stefan Repplinger

• Tommy Clausner

• Yaroslav Halchenko

Version 0.15 (2017-10-20)

Changelog

• mne.channels.Layout.plot() and mne.viz.plot_layout() now allows plotting a subset of channels with picks argument by Jaakko Leppakangas

• Add .bvef extension (BrainVision Electrodes File) to mne.channels.read_montage by Jean-Baptiste Schiratti

• Add mne.decoding.cross_val_multiscore() to allow scoring of multiple tasks, typically used with mne.decoding.SlidingEstimator, by Jean-Remi King

• Add mne.decoding.ReceptiveField module for modeling electrode response to input features by Chris Holdgraf

• Add mne.decoding.TimeDelayingRidge class, used by default by mne.decoding.ReceptiveField, to speed up auto- and cross-correlation computations and enable Laplacian regularization by Ross Maddox and Eric Larson

• Add new mne.datasets.mtrf dataset by Chris Holdgraf

• Add example of time-frequency decoding with CSP by Laura Gwilliams

• Add mne.decoding.SPoC to fit and apply spatial filters based on continuous target variables, by Jean-Remi King and Alexandre Barachant

• Add Fieldtrip’s electromyogram dataset, by Alexandre Barachant

• Add reject_by_annotation option to mne.preprocessing.find_eog_events() (which is also utilised by mne.preprocessing.create_eog_epochs()) to omit data that is annotated as bad by Jaakko Leppakangas

• Add example for fast screening of event-related dynamics in frequency bands by Denis Engemann

• Add mne.time_frequency.EpochsTFR.save() by Jaakko Leppakangas

• Add butterfly mode (toggled with ‘b’ key) to mne.io.Raw.plot() by Jaakko Leppakangas

• Add axes parameter to plot_topo functions by Jaakko Leppakangas

• Add options to change time windowing in mne.chpi.filter_chpi() by Eric Larson

• mne.channels.Montage.plot, mne.channels.DigMontage.plot(), and mne.viz.plot_montage() now allow plotting channel locations as a topomap by Clemens Brunner

• Add background_color parameter to mne.Evoked.plot_topo() and mne.viz.plot_evoked_topo() and improve axes rendering as done in mne.viz.plot_compare_evokeds() by Alex Gramfort

• Add support for GDF files in mne.io.read_raw_edf() by Nicolas Barascud

• Add mne.io.find_edf_events for getting the events as they are in the EDF/GDF header by Jaakko Leppakangas

• Speed up mne.io.Raw.plot() and mne.Epochs.plot() using (automatic) decimation based on low-passing with decim='auto' parameter by Eric Larson and Jaakko Leppakangas

• Add mne.inverse_sparse.mxne_optim.dgap_l21l1 for computing the duality gap for TF-MxNE as the new stopping criterion by Daniel Strohmeier

• Add option to return a list of Dipole objects in sparse source imaging methods by Daniel Strohmeier

• Add mne.inverse_sparse.make_stc_from_dipoles() to generate stc objects from lists of dipoles by Daniel Strohmeier

• Add mne.channels.find_ch_connectivity that tries to infer the correct connectivity template using channel info. If no template is found, it computes the connectivity matrix using Delaunay triangulation of the 2d projected channel positions by Jaakko Leppakangas

• Add IO support for EGI MFF format by Jaakko Leppakangas and ramonapariciog

• Add option to use matplotlib backend when plotting with mne.viz.plot_source_estimates() by Jaakko Leppakangas

• Add mne.channels.Montage.get_pos2d to get the 2D positions of channels in a montage by Clemens Brunner

• Add MGH 60- and 70-channel standard montages to mne.channels.read_montage by Eric Larson

• Add option for embedding SVG instead of PNG in HTML for mne.Report by Eric Larson

• Add confidence intervals, number of free parameters, and χ² to mne.fit_dipole() and mne.read_dipole() by Eric Larson

• mne.SourceEstimate.data is now writable, writing to it will also update mne.SourceEstimate.times by Marijn van Vliet

• mne.io.Raw.plot() and mne.Epochs.plot() now use anti-aliasing to draw signals by Clemens Brunner

• Allow using saved DigMontage to import digitization to mne.gui.coregistration() by Jaakko Leppakangas

• Add function mne.channels.get_builtin_montages() to list all built-in montages by Clemens Brunner

• mne.decoding.SlidingEstimator and mne.decoding.GeneralizingEstimator now accept **fit_params at fitting by Jean-Remi King

• Add mne.VectorSourceEstimate class which enables working with both source power and dipole orientations by Marijn van Vliet

• Add option pick_ori='vector' to mne.minimum_norm.apply_inverse() to produce mne.VectorSourceEstimate by Marijn van Vliet

• Add support for numpy.random.RandomState argument to seed in statistical clustering functions and better documentation of exact 1-sample tests by Eric Larson

• Extend mne.viz.plot_epochs_image()/mne.Epochs.plot_image() with regards to grouping by or aggregating over channels. See the new example at examples/visualization/plot_roi_erpimage_by_rt.py by Jona Sassenhagen

• Add bootstrapped confidence intervals to mne.viz.plot_compare_evokeds() by Jona Sassenhagen and Denis Engemann

• Add example on how to plot ERDS maps (also known as ERSP) by Clemens Brunner

• Add support for volume source spaces to spatial_src_connectivity and spatio_temporal_src_connectivity by Alex Gramfort

• Plotting raw data (mne.viz.plot_raw() or mne.io.Raw.plot()) with events now includes event numbers (if there are not more than 50 events on a page) by Clemens Brunner

• Add filtering functions mne.Epochs.filter() and mne.Evoked.filter(), as well as pad argument to mne.io.Raw.filter() by Eric Larson

• Add high frequency somatosensory MEG dataset by Jussi Nurminen

• Add reduced set of labels for HCPMMP-1.0 parcellation in mne.datasets.fetch_hcp_mmp_parcellation() by Eric Larson

• Enable morphing between hemispheres with mne.compute_morph_matrix by Christian Brodbeck

• Add return_residual to mne.minimum_norm.apply_inverse() by Eric Larson

• Add return_drop_log to mne.preprocessing.compute_proj_eog() and mne.preprocessing.compute_proj_ecg() by Eric Larson

• Add time cursor and category/amplitude status message into the single-channel evoked plot by Jussi Nurminen

BUG

• Fixed a bug when creating spherical volumetric grid source spaces in setup_volume_source_space() by improving the minimum-distance computations, which in general will decrease the number of used source space points by Eric Larson

• Fix bug in mne.io.read_raw_brainvision() read .vhdr files with ANSI codepage by Okba Bekhelifi and Alex Gramfort

• Fix unit scaling when reading in EGI digitization files using mne.channels.read_dig_montage by Matt Boggess

• Fix picks default in mne.io.Raw.filter() to include ref_meg channels by default by Eric Larson

• Fix mne.decoding.CSP order of spatial filter in patterns_ by Alexandre Barachant

• mne.concatenate_epochs() now maintains the relative position of events during concatenation by Alexandre Barachant

• Fix bug in script mne make_scalp_surfaces by Denis Engemann (this bug prevented creation of high-resolution meshes when they were absent in the first place.)

• Fix writing of raw files with empty set of annotations by Jaakko Leppakangas

• Fix bug in mne.preprocessing.ICA.plot_properties() where merging gradiometers would fail by Jaakko Leppakangas

• Fix mne.viz.plot_sensors() to maintain proper aspect ratio by Eric Larson

• Fix mne.viz.plot_topomap() to allow 0 contours by Jaakko Leppakangas

• Fix mne.preprocessing.ICA source-picking to increase threshold for rank estimation to 1e-14 by Jesper Duemose Nielsen

• Fix mne.set_bipolar_reference() to support duplicates in anodes by Jean-Baptiste Schiratti and Alex Gramfort

• Fix visuals of mne.viz.plot_evoked() and a bug where ylim changes when using interactive topomap plotting by Jaakko Leppakangas

• Fix mne.Evoked.plot_topomap() when using the mask argument with paired gradiometers by Eric Larson

• Fix bug in mne.Label.fill() where an empty label raised an error, by Eric Larson

• Fix mne.io.read_raw_ctf() to also include the samples in the last block by Jaakko Leppakangas

• Fix mne.preprocessing.ICA.save() to close file before attempting to delete it when write fails by Jesper Duemose Nielsen

• Fix mne.simulation.simulate_evoked() to use nave parameter instead of snr, by Yousra Bekhti

• Fix mne.read_bem_surfaces() for BEM files missing normals by Christian Brodbeck

• Fix mne.transform_surface_to() to actually copy when copy=True by Eric Larson

• Fix mne.io.read_raw_brainvision() to read vectorized data correctly by Jaakko Leppakangas and Phillip Alday

• Fix mne.connectivity.spectral_connectivity so that if n_jobs > 1 it does not ignore last n_epochs % n_jobs epochs by Mikołaj Magnuski

• Fix mne.io.read_raw_edf() to infer sampling rate correctly when reading EDF+ files where tal-channel has a higher sampling frequency by Jaakko Leppakangas

• Fix default value of kind='topomap' in mne.channels.Montage.plot to be consistent with mne.viz.plot_montage() by Clemens Brunner

• Fix bug in to_data_frame where non-consecutive picks would make the function crash by Jaakko Leppakangas

• Fix channel picking and drop in mne.time_frequency.EpochsTFR by Lukáš Hejtmánek

• Fix mne.SourceEstimate.transform() to properly update mne.SourceEstimate.times by Marijn van Vliet

• Fix mne.viz.plot_evoked_joint() to allow custom titles without appending information about the channels by Jaakko Leppakangas

• Fix writing a forward solution after being processed by mne.forward.restrict_forward_to_label() or mne.forward.restrict_forward_to_stc() by Marijn van Vliet

• Fix bug in mne.viz.plot_compare_evokeds() where truncate_yaxis was ignored (default is now False), by Jona Sassenhagen

• Fix bug in mne.viz.plot_evoked() where all xlabels were removed when using spatial_colors=True, by Jesper Duemose Nielsen

• Fix field mapping mne.make_field_map() and MEG bad channel interpolation functions (e.g., mne.Evoked.interpolate_bads()) to choose a better number of components during pseudoinversion when few channels are available, by Eric Larson

• Fix bug in mne.io.read_raw_brainvision(), changed default to read coordinate information if available and added test, by Jesper Duemose Nielsen

• Fix bug in mne.SourceEstimate.to_original_src() where morphing failed if two vertices map to the same target vertex, by Marijn van Vliet

• Fix mne.preprocessing.Xdawn to give verbose error messages about rank deficiency and handle transforming mne.Evoked, by Eric Larson

• Fix bug in DC and Nyquist frequency multitaper PSD computations, e.g. in mne.time_frequency.psd_multitaper, by Eric Larson

• Fix default padding type for mne.Epochs.resample() and mne.Evoked.resample() to be 'edge' by default, by Eric Larson

• Fix mne.inverse_sparse.mixed_norm(), mne.inverse_sparse.tf_mixed_norm() and mne.inverse_sparse.gamma_map() to work with volume source space and sphere head models in MEG by Alex Gramfort and Yousra Bekhti

• Fix mne.Evoked.as_type() channel renaming to append '_v' instead of '_virtual' to channel names to comply with shorter naming (15 char) requirements, by Eric Larson

• Fix treatment of CTF HPI coils as fiducial points in mne.gui.coregistration() by Eric Larson

• Fix resampling of events along with raw in mne.io.Raw() to now take into consideration the value of first_samp by Chris Bailey

• Fix labels of PSD plots in mne.viz.plot_raw_psd() by Alejandro Weinstein

• Fix depth weighting of sparse solvers (mne.inverse_sparse.mixed_norm(), mne.inverse_sparse.tf_mixed_norm() and mne.inverse_sparse.gamma_map()) with free orientation source spaces to improve orientation estimation by Alex Gramfort and Yousra Bekhti

• Fix the threshold in mne.beamformer.rap_music() to properly estimate the rank by Yousra Bekhti

• Fix treatment of vector inverse in mne.minimum_norm.apply_inverse_epochs() by Emily Stephen

• Fix mne.find_events() when passing a list as stim_channel parameter by Alex Gramfort

• Fix parallel processing when computing covariance with shrinkage estimators by Denis Engemann

API

• Removed the mne.datasets.megsim dataset because it was taken down by its host (MRN). Use the mne.simulation functions instead, by Eric Larson

• Add skip_by_annotation to mne.io.Raw.filter() to process data concatenated with e.g. mne.concatenate_raws() separately. This parameter will default to the old behavior (treating all data as a single block) in 0.15 but will change to skip_by_annotation='edge', which will separately filter the concatenated chunks separately, in 0.16. This should help prevent potential problems with filter-induced ringing in concatenated files, by Eric Larson

• ICA channel names have now been reformatted to start from zero, e.g. "ICA000", to match indexing schemes in mne.preprocessing.ICA and related functions, by Stefan Repplinger and Eric Larson

• Add mne.beamformer.make_lcmv() and mne.beamformer.apply_lcmv(), mne.beamformer.apply_lcmv_epochs(), and mne.beamformer.apply_lcmv_raw() to enable the separate computation and application of LCMV beamformer weights by Britta Westner, Alex Gramfort, and Denis Engemann.

• Add weight_norm parameter to enable both unit-noise-gain beamformer and neural activity index (weight normalization) and make whitening optional by allowing noise_cov=None in mne.beamformer.lcmv, mne.beamformer.lcmv_epochs, and mne.beamformer.lcmv_raw, by Britta Westner, Alex Gramfort, and Denis Engemann.

• Add new filtering mode fir_design='firwin' (default in the next 0.16 release) that gets improved attenuation using fewer samples compared to fir_design='firwin2' (default in the current 0.15 release) by Eric Larson

• Make the goodness of fit (GOF) of the dipoles returned by mne.beamformer.rap_music() consistent with the GOF of dipoles returned by mne.fit_dipole() by Alex Gramfort.

• mne.decoding.SlidingEstimator will now replace mne.decoding.TimeDecoding to make it generic and fully compatible with scikit-learn, by Jean-Remi King and Alex Gramfort

• mne.decoding.GeneralizingEstimator will now replace mne.decoding.GeneralizationAcrossTime to make it generic and fully compatible with scikit-learn, by Jean-Remi King and Alex Gramfort

• mne.viz.decoding.plot_gat_times, mne.viz.decoding.plot_gat_matrix are now deprecated. Use matplotlib instead as shown in the examples, by Jean-Remi King and Alex Gramfort

• Add norm_trace parameter to control single-epoch covariance normalization in :class:mne.decoding.CSP, by Jean-Remi King

• Allow passing a list of channel names as show_names in function mne.viz.plot_sensors() and methods mne.Evoked.plot_sensors(), mne.Epochs.plot_sensors() and mne.io.Raw.plot_sensors() to show only a subset of channel names by Jaakko Leppakangas

• Make function mne.io.eeglab.read_events_eeglab public to allow loading overlapping events from EEGLAB files, by Jona Sassenhagen.

• mne.find_events() mask_type parameter will change from 'not_and' to 'and' in 0.16.

• Instead of raising an error, duplicate channel names in the data file are now appended with a running number by Jaakko Leppakangas

• mne.io.read_raw_edf() has now 'auto' option for stim_channel (default in version 0.16) that automatically detects if EDF annotations or GDF events exist in the header and constructs the stim channel based on these events by Jaakko Leppakangas

• mne.io.Raw.plot_psd() now rejects data annotated bad by default. Turn off with reject_by_annotation=False, by Eric Larson

• mne.set_eeg_reference() and the related methods (e.g., mne.io.Raw.set_eeg_reference()) have a new argument projection, which if set to False directly applies an average reference instead of adding an SSP projector, by Clemens Brunner

• Deprecate plot_trans in favor of mne.viz.plot_alignment() and add bem parameter for plotting conductor model by Jaakko Leppakangas

• mne.beamformer.tf_lcmv now has a raw parameter to accommodate epochs objects that already have data loaded with preload=True, with mne.Epochs.load_data(), or that are read from disk, by Eric Larson

• mne.time_frequency.psd_welch and mne.time_frequency.psd_array_welch() now use a Hamming window (instead of a Hann window) by Clemens Brunner

• picks parameter in mne.beamformer.lcmv, mne.beamformer.lcmv_epochs, mne.beamformer.lcmv_raw, mne.beamformer.tf_lcmv and mne.beamformer.rap_music() is now deprecated and will be removed in 0.16, by Britta Westner, Alex Gramfort, and Denis Engemann.

• The keyword argument frequencies has been deprecated in favor of freqs in various time-frequency functions, e.g.