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 (acquisitions 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+