v1.2.rst

Version 1.2.0 (2022-10-11)

Enhancements

• Add vmin and vmax parameters to :meth:`mne.Evoked.animate_topomap` (:gh:`11073` by :newcontrib:`Mats van Es`)
• Enable common average reference projection for ECoG, sEEG, and DBS data (optionally jointly with joint=True) in :meth:`~mne.io.Raw.set_eeg_reference` and related functions/methods (:gh:`10656` by :newcontrib:`Moritz Gerster` and `Eric Larson`_)
• The trans parameter in :func:`mne.make_field_map` now accepts a :class:`~pathlib.Path` object, and uses standardised loading logic (:gh:`10784` by :newcontrib:`Andrew Quinn`)
• Add support for computing forward solutions using OpenMEEG_ (:gh:`11011` by `Alex Gramfort`_ and `Eric Larson`_)
• EEGLAB files (saved as MAT versions less than v7.3) can now be imported with :func:`mne.io.read_raw_eeglab` without the optional dependency pymatreader (:gh:`11006` by `Clemens Brunner`_)
• Add eight source estimate comparison metrics to new submodule :mod:`mne.simulation.metrics` (:gh:`6233` by `Kostiantyn Maksymenko`_ and `Alex Gramfort`_)
• Add :func:`mne.time_frequency.csd_tfr` to compute cross-spectral density from :class:`mne.time_frequency.EpochsTFR` (:gh:`10986` by `Alex Rockhill`_)
• Improve repr() for :class:`mne.minimum_norm.InverseOperator` when loose orientation is used (:gh:`11048` by `Eric Larson`_)
• Add support for vector and volume source estimates in :func:`mne.minimum_norm.get_point_spread` and :func:`mne.minimum_norm.get_cross_talk` (:gh:`8639`, :gh:`11083` by `Olaf Hauk`_, `Marijn van Vliet`_, `Alex Gramfort`_, and `Eric Larson`_)
• :meth:`mne.Epochs.plot_psd_topomap` now suppresses redundant colorbars when vlim='joint' (:gh:`11051` by `Daniel McCloy`_)
• Add starting_affine keyword argument to :func:`mne.transforms.compute_volume_registration` to initialize an alignment with an affine (:gh:`11020` by `Alex Rockhill`_)
• Add HTML representation for ~mne.Evoked in Jupyter Notebooks (:gh:`11075` by `Valerii Chirkov`_ and `Andrew Quinn`_)
• Add support for temperature and gsr (galvanic skin response, i.e., electrodermal activity) channel types (:gh:`11090`, :gh:`11108` by `Eric Larson`_ and `Richard Höchenberger`_)
• Allow :func:`mne.beamformer.make_dics` to take pick_ori='vector' to compute vector source estimates (:gh:`10980` by `Alex Rockhill`_)
• Add units parameter to :func:`mne.io.read_raw_edf` in case units are missing from the file (:gh:`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 (:gh:`11077` by `Andrew Quinn`_)
• Improve interpolation of bridged electrodes with ~mne.preprocessing.interpolate_bridged_electrodes (:gh:`11094` by `Mathieu Scheltienne`_)
• Add :func:`mne.minimum_norm.apply_inverse_tfr_epochs` to apply inverse methods to time-frequency resolved epochs (:gh:`11095` by `Alex Rockhill`_)
• Add support for multiple probes via multiple CSV files passed to :func:`mne.io.read_raw_hitachi` (:gh:`11186` by `Eric Larson`_)
• Add :func:`mne.chpi.get_active_chpi` to retrieve the number of active hpi coils for each time point (:gh:`11122` by `Eduard Ort`_)
• Add example of how to obtain time-frequency decomposition using narrow bandpass Hilbert transforms to :ref:`ex-tfr-comparison` (:gh:`11116` by `Alex Rockhill`_)
• Add == and != comparison between mne.Projection objects (:gh:`11147` by `Mathieu Scheltienne`_)
• Parse automatically temperature channel with :func:`mne.io.read_raw_edf` (:gh:`11150` by `Eric Larson`_ and `Alex Gramfort`_)
• Add unscale option to :func:`mne.head_to_mri` to facilitate working with surrogate MRI data (:gh:`11185` by `Eric Larson`_)
• Add encoding parameter to :func:`mne.io.read_raw_edf` and :func:`mne.io.read_raw_bdf` to support custom (non-UTF8) annotation channel encodings (:gh:`11154` by `Clemens Brunner`_)
• :class:`mne.preprocessing.ICA` gained a new method, :meth:`~mne.preprocessing.ICA.get_explained_variance_ratio`, that allows the retrieval of the proportion of variance explained by ICA components (:gh:`11141` by `Richard Höchenberger`_)
• Add on_baseline to :meth:`mne.preprocessing.ICA.apply`, :meth:`mne.preprocessing.ICA.plot_overlay`, and :func:`mne.viz.plot_ica_overlay` to allow reapplying baseline correction after applying ICA (:gh:`11232` by `Eric Larson`_)
• Add config option MNE_REPR_HTML to disable HTML repr in notebook environments (:gh:`11159` by `Clemens Brunner`_)

Bugs

• Fix bug in :meth:`mne.io.Raw.crop` where argument include_tmax was not considered in checking tmax in bounds (:gh:`11196` by `Lukas Gemein`_)
• Fix bug in :func:`mne.io.read_raw_eeglab` where unlabeled fiducials caused reading errors (:gh:`11074` by :newcontrib:`Sebastiaan Mathot`)
• Fix bug in :func:`mne.time_frequency.read_csd` that returned projs as a list of dict instead of :class:`mne.Projection` (:gh:`11072` by :newcontrib:`Chetan Gohil`)
• Fix bug in :func:`mne.decoding.TimeFrequency` that prevented cloning if constructor arguments were modified (:gh:`11004` by :newcontrib:`Daniel Carlström Schad`)
• Fix bug in repr of decoding estimator classes (e.g., :class:`mne.decoding.SlidingEstimator`) where the parameters where not stored in the result string but instead just printed to sys.stdout (:gh:`11190` by :newcontrib:`Dominik Wetzel`)
• Document height and weight keys of subject_info entry in :class:`mne.Info` (:gh:`11019` by :newcontrib:`Sena Er`)
• Fix bug in :class:`mne.viz.Brain` constructor where the first argument was named subject_id instead of subject (:gh:`11049` by `Eric Larson`_)
• Fix bug in :ref:`mne coreg` where the MEG helmet position was not updated during ICP fitting (:gh:`11084` by `Eric Larson`_)
• Fix bug in :func:`~mne.io.read_raw_curry`, and :func:`~mne.io.read_raw_cnt` where digitization points were not read properly (:gh:`11145` by `Eric Larson`_)
• Fix bug in :func:`mne.minimum_norm.apply_inverse_epochs` where the average EEG projector was not checked properly (:gh:`11182` by `Eric Larson`_)
• Fix bug in :func:`mne.viz.plot_filter` when plotting filters created using output='ba' mode with compensation turned on. (:gh:`11040` by `Marian Dovgialo`_)
• Fix bugs in documentation of surface :class:`~mne.SourceSpaces` (:gh:`11171` by `Eric Larson`_)
• Fix bug in :func:`mne.viz.plot_compare_evokeds` where automatic legend labels could be excessively long; they are now abbreviated with ... when necessary (:gh:`11181` by `Eric Larson`_)
• Fix bugs with verbose='error' not being used properly and allowing warnings through (:gh:`11193` by `Eric Larson`_)
• Fix bug in :func:`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 (:gh:`11102` by `Eric Larson`_)
• Fix bug in :func:`mne.viz.plot_topomap` when providing sphere="eeglab" (:gh:`11081` by `Mathieu Scheltienne`_)
• Fix bug in :meth:`mne.Dipole.to_mri` where MRI RAS rather than MRI surface RAS was returned (:gh:`11185` by `Eric Larson`_)
• Fix bug in :meth:`epochs.save <mne.Epochs.save>` where the verbose parameter defaulted to True instead of None (:gh:`11191` by `Eric Larson`_)
• The string and HTML representation of :class:`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 :meth:`~mne.preprocessing.ICA.get_explained_variance_ratio` method (:gh:`11141` by `Richard Höchenberger`_)
• Fix bug in :meth:`mne.Evoked.plot` and related methods where a np.nan location value in any channel causes spatial colours to fail (:gh:`6870` by `Simeon Wong`_)
• Fix bug in :meth:`mne.preprocessing.ICA.find_bads_muscle` where epochs caused an error when passed as the inst (:gh:`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 (:gh:`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 (:gh:`11203` by `Richard Höchenberger`_)
• Fix bug in :meth:`mne.Report.add_ica` and where baselines were not reapplied to the data when inst is Epochs or Evoked (:gh:`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 (:gh:`11201` by :newcontrib:`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 (:gh:`11120` by `Daniel McCloy`_)
• The names parameter of :func:`mne.viz.plot_arrowmap` and :func:`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 (:gh:`11123` by `Daniel McCloy`_)
• The bands parameter of :meth:`mne.Epochs.plot_psd_topomap` now accepts :class:`dict` input; legacy :class:`tuple` input is supported, but discouraged for new code (:gh:`11050` by `Daniel McCloy`_)
• The :func:`mne.head_to_mri` new function parameter kind default will change from 'ras' to 'mri' (:gh:`11185` by `Eric Larson`_)
• The show_toolbar argument to :class:`mne.viz.Brain` is being removed by deprecation (:gh:`11049` by `Eric Larson`_)
• New classes :class:`~mne.time_frequency.Spectrum` and :class:`~mne.time_frequency.EpochsSpectrum`, created via new methods :meth:`Raw.compute_psd()<mne.io.Raw.compute_psd>`, :meth:`Epochs.compute_psd()<mne.Epochs.compute_psd>`, and :meth:`Evoked.compute_psd()<mne.Evoked.compute_psd>` (:gh:`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 (:gh:`11123` by `Daniel McCloy`_)
• In :func:`mne.viz.plot_topomap`, passing axes=None will now create a new :class:`~matplotlib.figure.Figure` instead of plotting into the current axes (:gh:`11123` by `Daniel McCloy`_)
• In :func:`mne.viz.plot_topomap`, the parameter show_names has been deprecated, use the names parameter instead (:gh:`11123` by `Daniel McCloy`_)
• In :func:`mne.viz.plot_topomap`, :func:`~mne.viz.plot_tfr_topomap`, :func:`~mne.viz.plot_evoked_topomap`, and related class methods :meth:`mne.Covariance.plot_topomap`, :meth:`mne.Evoked.plot_topomap`, and :meth:`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 (:gh:`11123` by `Daniel McCloy`_)
• In :func:`mne.viz.plot_tfr_topomap`, :func:`~mne.viz.plot_evoked_topomap`, and related class methods :meth:`mne.Covariance.plot_topomap`, :meth:`mne.Evoked.plot_topomap`, and :meth:`mne.time_frequency.AverageTFR.plot_topomap`: the title parameter has been deprecated; use matplotlib's :meth:`fig.suptitle()<matplotlib.figure.Figure.suptitle>` instead (:gh:`11123` by `Daniel McCloy`_)
• In functions/methods for plotting topomaps, the outlines='skirt' option is deprecated; use sphere='eeglab' for similar functionality (:gh:`11123` by `Daniel McCloy`_)
• The mne.epochs.add_channels_epochs function has been deprecated in favor of :meth:`epochs.add_channels <mne.Epochs.add_channels>` (:gh:`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 :class:`~mne.time_frequency.Spectrum` or :class:`~mne.time_frequency.EpochsSpectrum` objects instead and then run spectrum.get_data(return_freqs=True) (:gh:`10184` by `Daniel McCloy`_)
• Added new class :class:`mne.preprocessing.EOGRegression` to allow more flexibility when using regression to reduce EOG artifacts (:gh:`11046` by `Marijn van Vliet`_)
• New parameter exclude added to :func:`mne.preprocessing.regress_artifact` to prevent regression from being applied to certain channels (:gh:`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+