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Version 0.24.0 (2021-11-03)

Enhancements

  • Add pooch to system information reports (:gh:`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 (:gh:`9575` by new contributor |Darin Erat Sleiter|_)
  • Add support for NIRSport and NIRSport2 devices to mne.io.read_raw_nirx (:gh:`9348` and :gh:`9401` by new contributor |David Julien|_, new contributor |Romain Derollepot|_, `Robert Luke`_, and `Eric Larson`_)
  • New function :func:`mne.Dipole.to_volume_labels` to get atlas label for MRI coordinates. (:gh:`9376` by new contributor |Marian Dovgialo|_)
  • Add support for SURE parameter selection in :func:`mne.inverse_sparse.mixed_norm` and make alpha parameter now default to 'sure' (:gh:`9430` by new contributor |Pierre-Antoine Bannier|_ and `Alex Gramfort`_)
  • Speed up BCD solver in :func:`mne.inverse_sparse.mixed_norm` by adding Anderson acceleration (:gh:`9481` by new contributor |Pierre-Antoine Bannier|_ and `Alex Gramfort`_)
  • Add support for list of channel types for EEG/sEEG/ECoG/DBS referencing (:gh:`9637` by new contributor |Mathieu Scheltienne|_)
  • Add the ability to set point size and line width in :func:`mne.viz.plot_sensors` and related functions (:gH:`9872` by new contributor |Dominique Makowski|_)
  • Add support for changing the default event id used by :func:`mne.make_fixed_length_epochs` (:gh:`9782` by new contributor |Mathieu Scheltienne|_)
  • Improve documentation for arguments threshold, method and measure of ICA methods ~mne.preprocessing.ICA.find_bads_ecg, ~mne.preprocessing.ICA.find_bads_ref and ~mne.preprocessing.ICA.find_bads_eog (:gh:`9858` by new contributor |Mathieu Scheltienne|_)
  • Add support for more than 3 source estimates in :func:`mne.viz.plot_sparse_source_estimates` (:gh:`9640` by new contributor |Pierre-Antoine Bannier|_ and `Alex Gramfort`_)
  • Add cortical signal suppression (CSS) :func:`mne.preprocessing.cortical_signal_suppression` (:gh:`6888`, :gh:`9892` by new contributor |John Samuelsson|_ and `Eric Larson`_)
  • Show all good channel types and counts when printing a :class:`mne.Info` in the notebook (:gh:`9725` by `Valerii Chirkov`_ and `Eric Larson`_)
  • Speed up point decimation in :func:`mne.io.read_raw_kit` by vectorization and use of :class:`scipy.spatial.cKDTree` (:gh:`9568` by `Jean-Rémi King`_ and `Eric Larson`_)
  • Add ability to export EDF+ files using :func:`mne.export.export_raw` (:gh:`9643` by `Adam Li`_)
  • New function :func:`mne.chpi.get_chpi_info` to retrieve basic information about the cHPI system used when recording MEG data (:gh:`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 (:gh:`9427` by `Eric Larson`_)
  • Add support for Hitachi fNIRS devices in mne.io.read_raw_hitachi (:gh:`9391` by `Eric Larson`_)
  • Add support for picks in :func:`mne.stc_near_sensors` (:gh:`9396` by `Eric Larson`_)
  • Add label methods mne.Label.compute_area and mne.Label.distances_to_outside (:gh:`9424` by `Eric Larson`_)
  • Add projections when printing a :class:`mne.Info` in the notebook (:gh:`9403` by `Alex Gramfort`_)
  • Add new function :func:`mne.bem.make_scalp_surfaces` to compute scalp surfaces for coregistration (:gh:`9463` by `Alex Gramfort`_)
  • Add support for interpolating oxy and deoxyhaemoglobin data types (:gh:`9431` by `Robert Luke`_)
  • Add support for SNIRF files in :class:`mne.Report` (:gh:`9443` by `Robert Luke`_)
  • Add support for exporting MFF evoked files using mne.export.export_evokeds and mne.export.export_evokeds_mff (:gh:`9406` by `Evan Hathaway`_)
  • :func:`mne.concatenate_raws`, :func:`mne.concatenate_epochs`, and :func:`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 (:gh:`9438` by `Richard Höchenberger`_)
  • Add support for multiple datablocks (acquisitions with pauses) in :func:`mne.io.read_raw_nihon` (:gh:`9437` by `Federico Raimondo`_)
  • Add new function :func:`mne.preprocessing.annotate_break` to automatically detect and mark "break" periods without any marked experimental events in the continuous data (:gh:`9445` by `Richard Höchenberger`_)
  • Add "time_format" to :meth:`mne.io.Raw.plot` and :meth:`mne.preprocessing.ICA.plot_sources` to display acquisition time on x-axis (:gh:`9419` by `Martin Schulz`_)
  • Speed up :meth:`mne.decoding.TimeDelayingRidge.predict` by switching to FFT-based convolution (:gh:`9458` by `Ross Maddox`_)
  • Show multiple colors and linestyles for excluded components with :class:`mne.Evoked` in :meth:`mne.preprocessing.ICA.plot_sources` (:gh:`9444` by `Martin Schulz`_)
  • Add functions for aligning MRI and CT data mne.transforms.compute_volume_registration and mne.transforms.apply_volume_registration (:gh:`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 :ref:`tut-ieeg-localize` (:gh:`9484` by `Alex Rockhill`_)
  • Add vertex number in source space for :meth:`mne.VolSourceEstimate.plot` and :func:`mne.viz.plot_volume_source_estimates` (:gh:`9697` by `Eric Larson`_)
  • Add support for colormap normalization in :func:`mne.viz.plot_topomap` (:gh:`9468` by `Clemens Brunner`_)
  • Update :func:`mne.preprocessing.realign_raw` with Numpy-recommended polynomial fitting method (:gh:`9514` by `Erica Peterson`_)
  • Add a warning to mne.preprocessing.nirs.beer_lambert_law when source-detector distances are zero (:gh:`9541` by `Eric Larson`_)
  • Add exclude parameter to :meth:`mne.io.Raw.plot_psd` and :meth:`mne.Epochs.plot_psd` (:gh:`9519` by `Clemens Brunner`_)
  • Add mne.Annotations.rename to rename annotation descriptions (:gh:`9525` by `Robert Luke`_)
  • Add mne.Annotations.set_durations to set annotation durations (:gh:`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 (:gh:`9558` by `Clemens Brunner`_)
  • Add :meth:`mne.Evoked.get_data` method to :class:`mne.Evoked` (:gh:`9555` by `Stefan Appelhoff`_)
  • The :meth:`mne.Epochs.get_data` method now has a units parameter (:gh:`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 (:gh:`9544` by `Alex Rockhill`_)
  • :meth:`mne.io.Raw.get_data`, :meth:`mne.Epochs.get_data`, and :meth:`mne.Evoked.get_data` methods now have tmin and tmax parameters to specify data window in seconds to get (:gh:`9556` by `Stefan Appelhoff`_)
  • The :meth:`mne.Evoked.get_data` method now has a units parameter (:gh:`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 (:gh:`9570` by `Daniel McCloy`_ and `Jussi Nurminen`_)
  • Add :func:`mne.get_montage_volume_labels` to find the regions of interest in a Freesurfer atlas anatomical segmentation for an intracranial electrode montage and :func:`mne.viz.plot_channel_labels_circle` to plot them (:gh:`9545` by `Alex Rockhill`_)
  • Add :func:`mne.viz.Brain.add_volume_labels` to plot subcortical surfaces and other regions of interest (:gh:`9540` by `Alex Rockhill`_ and `Eric Larson`_)
  • Add custom cortex curvature colors in :class:`mne.viz.Brain` via the cortex argument (:gh:`9750` by `Eric Larson`_)
  • Add :meth:`mne.channels.DigMontage.apply_trans` to apply a transform directly to a montage (:gh:`9601` by `Alex Rockhill`_)
  • :meth:`mne.preprocessing.ICA.fit` now emits a warning if any of the start, stop, reject, and flat parameters are passed when performing ICA on ~mne.Epochs. These parameters only have an effect on ~mne.io.Raw data and were previously silently ignored in the case of ~mne.Epochs (:gh:`9605` by `Richard Höchenberger`_)
  • :func:`mne.viz.plot_alignment` now emits a warning (instead of aborting with an exception) if the surfaces contain topological defects (:gh:`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 (:gh:`9614` by `Richard Höchenberger`_)
  • New :class:`mne.coreg.Coregistration` object to allow coregistration scripting without a dependency on mayavi (:gh:`9516` by `Guillaume Favelier`_).
  • Add :meth:`mne.viz.Brain.add_head` to plot the head surface (:gh:`9618` by `Alex Rockhill`_)
  • Add :func:`mne.channels.read_dig_localite` to read Localite electrode location files (:gh:`9658` by `Clemens Brunner`_)
  • Add :meth:`mne.viz.Brain.add_sensors` to plot sensor locations (:gh:`9585` by `Alex Rockhill`_)
  • Add :func:`mne.coreg.estimate_head_mri_t` to estimate the head->mri transform from fsaverage fiducials (:gh:`9585` by `Alex Rockhill`_)
  • Add :meth:`mne.channels.DigMontage.add_mni_fiducials` to add fiducials to a montage in MNI coordinates (:gh:`9682` by `Alex Rockhill`_)
  • Add :meth:`mne.channels.DigMontage.remove_fiducials` to remove fiducials under rare circumstances when the coordinate frame should not be set to "head" (:gh:`9684` by `Alex Rockhill`_)
  • Add remove methods for mesh objects in :class:`mne.viz.Brain` (:gh:`9688` by `Alex Rockhill`_)
  • Add --show-paths and --developer options to :ref:`mne sys_info` (:gh:`9789` by `Eric Larson`_)
  • Add ability to export EDF+ files using :func:`mne.export.export_raw` (:gh:`9643` by `Adam Li`_)
  • Reading EDF files via :func:`mne.io.read_raw_edf` now can infer channel type from the signal label in the EDF header (:gh:`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 :class:`mne.Info` object (:gh:`9586` by `Alex Rockhill`_)
  • All data fetching code now relies on pooch, which is an added optional requirement for dataset fetchers (:gh:`9742` by `Adam Li`_ and `Daniel McCloy`_)
  • Add phantom FreeSurfer subject fetcher :func:`mne.datasets.fetch_phantom` to allow fetching the Otaniemi phantom (:gh:`9796` by `Eric Larson`_)
  • Add :func:`mne.datasets.fetch_dataset` to allow packages to fetch datasets in a similar fashion to MNE (:gh:`9763` by `Adam Li`_)
  • Add full ECoG dataset to MNE-misc-data and demonstrate its use in :ref:`ex-electrode-pos-2d` and :ref:`tut-ieeg-localize` (:gh:`9784` by `Alex Rockhill`_)
  • Add options tol and accuracy to :func:`mne.fit_dipole` to control optimization (:gh:`9810` by `Eric Larson`_)
  • Completely revamp the ~mne.Report experience: new HTML layout, many new methods, more flexibility; the functionality is demonstrated in :ref:`tut-report` (:gh:`9754`, :gh:`9828`, :gh:`9847`, :gh:`9860`, :gh:`9861`, :gh:`9862`, :gh:`9863`, :gh:`9871`, :gh:`9881`, :gh:`9891`, :gh:`9901` by `Richard Höchenberger`_, `Eric Larson`_, and `Alex Gramfort`_)
  • Add basic HTML representations of ~mne.Forward and ~mne.minimum_norm.InverseOperator instances for a nicer Jupyter experience (:gh:`9754` by `Richard Höchenberger`_)
  • mne.io.read_raw_brainvision now handles ASCII data with comma-separated values, as may be exported from BrainVision Analyzer (:gh:`9795` by `Richard Höchenberger`_)
  • Add :func:`mne.preprocessing.ieeg.project_sensors_onto_brain` to project ECoG sensors onto the pial surface to compensate for brain shift (:gh:`9800` by `Alex Rockhill`_)
  • Add support for data acquired with NIRx devices using Aurora software version 2021.9 (:gh:`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! (:gh:`9613`, :gh:`9845` by `Richard Höchenberger`_)
  • All functions accepting a FreeSurfer subjects directory via a subjects_dir parameter can now consume :class:`pathlib.Path` objects too (used to be only strings) (:gh:`9613` by `Richard Höchenberger`_)
  • Add support for colormap normalization in :meth:`mne.time_frequency.AverageTFR.plot` (:gh:`9851` by `Clemens Brunner`_)
  • Add support for BIDS-compatible filenames when splitting big epochs files via the new split_naming parameter in :meth:`mne.Epochs.save` (:gh:`9869` by `Denis Engemann`_)
  • Add by_event_type parameter to :meth:`mne.Epochs.average` to create a list containing an :class:`mne.Evoked` object for each event type (:gh:`9859` by `Marijn van Vliet`_)
  • Add pyqtgraph as a new backend for :meth:`mne.io.Raw.plot` (:gh:`9687` by `Martin Schulz`_)
  • Add :func:`mne.viz.set_browser_backend`, :func:`mne.viz.use_browser_backend` and :func:`mne.viz.get_browser_backend` to set matplotlib or pyqtgraph as backend for :meth:`mne.io.Raw.plot` (:gh:`9687` by `Martin Schulz`_)

Bugs

  • Fix bug in :meth:`mne.io.Raw.pick` and related functions when parameter list contains channels which are not in info instance (:gh:`9708` by new contributor |Evgeny Goldstein|_)
  • Fix a few typos (:gh:`9706` by new contributor |Timothy Gates|_)
  • Fix bug with :meth:`mne.Epochs.crop` and :meth:`mne.Evoked.crop` when include_tmax=False, where the last sample was always cut off, even when tmax > epo.times[-1] (:gh:`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 (:gh:`9381`, :gh:`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 (:gh:`9719` by new contributor |Mathieu Scheltienne|_)
  • Fix bug with :func:`mne.concatenate_epochs` where the concatenated events could end up in non-chronological order. (:gh:`9765` by new contributor |Jan Sosulski|_)
  • Fix bug where :func:`mne.time_frequency.psd_array_welch` and :func:`mne.time_frequency.psd_array_multitaper` failed to handle negative integer for n_jobs argument (:gh:`9849` by new contributor |Riessarius Stargardsky|_)
  • Fix bug where resampling returns empty instances (:gh:`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. (:gh:`9920` by new contributor |Mathieu Scheltienne|_)
  • Fix bug with :func:`mne.io.read_raw_nihon` where latin-1 annotations could not be read (:gh:`9384` by `Alex Gramfort`_)
  • Fix bug when printing a :class:`mne.io.RawArray` in the notebook (:gh:`9404` by `Alex Gramfort`_)
  • Fix bug when computing rank from info for SSS data with only gradiometers or magnetometers (:gh:`9435` by `Alex Gramfort`_)
  • Fix bug with mne.preprocessing.find_bad_channels_maxwell where all-flat segments could lead to an error (:gh:`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 (:gh:`9447` by `Eric Larson`_)
  • Fix bug with mne.io.read_raw_fieldtrip and mne.read_epochs_fieldtrip where channel positions were not set properly (:gh:`9447` by `Eric Larson`_)
  • Fix bug with :func:`mne.io.read_raw_kit` where omitting HPI coils could lead to an :exc:`python:AssertionError` on reading (:gh:`9612` by `Eric Larson`_)
  • Fix bug with :func:`mne.io.read_raw_edf` where reading only stimulus channels would lead to an error (:gh:`9831` by `Eric Larson`_)
  • Fix bug with mne.preprocessing.nirs.optical_density where protection against zero values was not guaranteed (:gh:`9522` by `Eric Larson`_)
  • :func:`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 (:gh:`9438` by `Richard Höchenberger`_)
  • Fixed bug in :meth:`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 (:gh:`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 (:gh:`#9513` by `Eric Larson`_)
  • In :func:`mne.viz.plot_ica_scores` and :meth:`mne.preprocessing.ICA.plot_scores`, the figure and axis titles no longer overlap when plotting only a single EOG or ECG channel (:gh:`9489` by `Richard Höchenberger`_).
  • Ensure mne.io.Raw.get_montage works with SNIRF data (:gh:`9524` by `Robert Luke`_)
  • Fix bug in :func:`mne.setup_volume_source_space` where non-finite positions could be used in a discrete source space (:gh:`9603` by `Eric Larson`_)
  • Fix bug in :func:`mne.viz.plot_topomap` (and related methods like :meth:`mne.Evoked.plot_topomap`) where large distances between electrodes (higher than head radius) would lead to an error (:gh:`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 (:gh:`9558` by `Eric Larson`_)
  • Fix bug in :func:`mne.make_forward_solution` where impossible sensor-BEM geometries were not checked (:gh:`9893` by `Eric Larson`_)
  • Fix bug in :func:`mne.concatenate_epochs` when concatenating :class:`mne.Epochs` objects with 0 events (:gh:`9535` by `Marijn van Vliet`_)
  • Fix bug in :func:`mne.viz.Brain.screenshot` where the RGBA mode was not supported (:gh:`9564` by `Guillaume Favelier`_).
  • Fix bug in :func:`mne.io.read_raw_egi` where reading data from a data segment that is part of an acquisition skip would lead to an error (:gh:`9565` by `Eric Larson`_)
  • Prevent :meth:`mne.io.Raw.plot` windows from spawning at sizes too small to properly render (:gh:`9629` by `Daniel McCloy`_)
  • Fix bug where :meth:`mne.io.Raw.plot` raised an error when plotting raw dipole data (:gh:`9771` by `Eric Larson`_)
  • Fix bug in ::meth:`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 (:gh:`9556` by `Stefan Appelhoff`_)
  • Fix bug in :func:`mne.viz.set_3d_backend` and :func:`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 :func:`mne.viz.get_3d_backend` instead of 'pyvista', and consider using get_3d_backend().startswith('pyvista') for example for backward-compatible conditionals (:gh:`9607` by `Guillaume Favelier`_)
  • Fix bug in :func:`mne.viz.plot_compare_evokeds` where confidence bands were not drawn if only one condition was plotted (:gh:`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" (:gh:`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" (:gh:`9580` by `Alex Rockhill`_)
  • Raise error when no trans is provided to :func:`mne.viz.plot_alignment` when required instead of assuming identity head->mri transform (:gh:`9585` by `Alex Rockhill`_)
  • Fix bug where :meth:`mne.Epochs.equalize_event_counts` failed when only one good epoch existed for one of the event types (:gh:`9758` by `Daniel McCloy`_)
  • Fix bug where channels with a dollar sign ($) were not being labeled "misc" in :func:`mne.io.read_raw_nihon` (:gh:`9695` by `Adam Li`_)
  • Fix bug where :func:`mne.io.read_raw_persyst` was lower-casing events it found in the .lay file (:gh:`9746` by `Adam Li`_)
  • Fix bug with Qhull when plotting OPM sensors in :func:`mne.viz.plot_alignment` (:gh:`9799` and :gh:`9804` by `Eric Larson`_)
  • Fix bug where :func:`mne.io.read_raw_snirf` was including the landmark index as a spatial coordinate (:gh:`9777` by `Robert luke`_)
  • Fix bug where mne.Annotations were not appending channel names when being added together (:gh:`9780` by `Adam Li`_)
  • mne.viz.plot_evoked_joint now correctly handles a times='peaks' parameter value (:gh:`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 (:gh:`9754` by `Richard Höchenberger`_)
  • Fix a bug with :func:`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 (:gh:`9933` by `Eric Larson`_)
  • In :meth:`mne.io.Raw.plot_psd` and :meth:`mne.Epochs.plot_psd`, avoid overlap between subplot titles and x-axis tick labels (:gh:`9864` by `Richard Höchenberger`_)
  • In :meth:`mne.Epochs.plot_psd_topomap`, the data is now scaled to match the output of :meth:`mne.Epochs.plot_psd` (:gh:`9873` by `Richard Höchenberger`_)
  • Fix channel locations with NaN values causing all channel locations not to be plotted in :func:`mne.viz.Brain.add_sensors` (:gh:`9911` by `Alex Rockhill`_)
  • Fix infinite loop bug in :func:`mne.get_montage_volume_labels` (:gh:`9940` by `Alex Rockhill`_)

API changes

  • The :class:`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 :class:`mne.Info` for more information (:gh:`9867` by new contributor |Mathieu Scheltienne|_)
  • The Mayavi 3D backend has been deprecated (:gh:`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 :ref:`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 :ref:`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 (:gh:`9505` by `Alex Rockhill`_ and `Eric Larson`_)
  • Split :func:`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 (:gh:`9596` by `Alex Rockhill`_)
  • Deprecate solver='prox' in :func:`mne.inverse_sparse.mixed_norm` in favor of solver='cd' and solver='bcd' as coordinate descent solvers consistently outperform proximal gradient descent (:gh:`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 (:gh:`9493` by `Adam Li`_).
  • :func:`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 (:gh:`9685` by `Alex Gramfort`_)
  • Deprecate functions :samp:`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 :func:`mne.datasets.has_dataset` instead (:gh:`9781` by `Daniel McCloy`_ and `Adam Li`_)
  • :class:`mne.Report` modernization has led to multiple deprecations (:gh:`9754` by `Richard Höchenberger`_):
    • mne.Report.add_figs_to_section and mne.Report.add_slider_to_section have been deprecated in favor of :meth:`mne.Report.add_figure`
    • mne.Report.add_images_to_section has been deprecated in favor of :meth:`mne.Report.add_image`
    • mne.Report.add_bem_to_section has been deprecated in favor of :meth:`mne.Report.add_bem`
    • mne.Report.add_htmls_to_section has been deprecated in favor of :meth:`mne.Report.add_html`
    • In :meth:`mne.Report.parse_folder`, the sort_sections parameter has been deprecated in favor of sort_content
    • In :meth:`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
  • :meth:`mne.Epochs.plot` and :func:`mne.viz.plot_epochs` gained parameter show_scalebars analogous to :meth:`mne.viz.plot_raw` (:gh:`9815` by `Daniel McCloy`_)
  • The output folder name for HF_SEF datasets is now hf_sef instead of HF_SEF (:gh:`9763` by `Adam Li`_)
  • Deprecate mne.viz.utils.center_cmap (:gh:`9851` by `Clemens Brunner`_)
  • The default partial pathlength factor of :func:`mne.preprocessing.nirs.beer_lambert_law` will change from 0.1 in 0.24 to 6.0 in the next release (:gh:`9843` by `Robert Luke`_)
  • mne.preprocessing.ICA.detect_artifacts has been deprecated. Please use ~mne.preprocessing.ICA.find_bads_eog and ~mne.preprocessing.ICA.find_bads_ecg instead (:gh:`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-Rémi 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+