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 Evgenii 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-Rémi 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 +