v1.3.rst

Version 1.3.0 (2022-12-21)

Enhancements

• Improve default line width used in :func:`mne.viz.plot_filter` (:gh:`11333` by :newcontrib:`Toomas Erik Anijärv`)
• Add the argument max_iter to :func:`~mne.time_frequency.psd_array_multitaper` and to :func:`~mne.time_frequency.csd_array_multitaper` to increase the maximum number of iterations to reach convergence when using adaptive=True (:gh:`11237` by `Mathieu Scheltienne`_)
• Add a warning to the docstring of :func:`mne.channels.find_ch_adjacency` to encourage users to validate their outputs (:gh:`11236` by `Felix Klotzsche`_ and `Eric Larson`_)
• Mixed, cortical + discrete source spaces with fixed orientations are now allowed. (:gh:`11241` by `Jevri Hanna`_)
• Add size information to the repr of :class:`mne.Report` (:gh:`11357` by `Eric Larson`_)
• Add support for image_format='webp' to :class:`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 (:gh:`11359` by `Eric Larson`_)
• Add :func:`mne.beamformer.apply_dics_tfr_epochs` to apply a DICS beamformer to time-frequency resolved epochs (:gh:`11096` by `Alex Rockhill`_)
• Add :func:`mne.time_frequency.fwhm` to determine the full-width half maximum for :func:`mne.time_frequency.morlet` (:gh:`11353` by `Britta Westner`_, `Daniel McCloy`_, and `Eric Larson`_)
• Check whether head radius (estimated from channel positions) is correct when reading EEGLAB data with :func:`~mne.io.read_raw_eeglab` and :func:`~mne.read_epochs_eeglab`. If head radius is not within likely values, warn informing about possible units mismatch and the new montage_units argument (:gh:`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 (:gh:`11329` by `Mathieu Scheltienne`_)

Bugs

• Fix bug in :func:`mne.export.export_raw` when exporting raw to EDF with EDFLib when subject sex is missing (:gh:`11375` by :newcontrib:`Mark Alexander Henney`)
• Fix bugs in documentation of :func:`mne.time_frequency.tfr_array_multitaper` and related functions/methods (:gh:`11310` by :newcontrib:`Santeri Ruuskanen`)
• Fix bug to be able to customize legends when using :meth:`mne.viz.Brain.add_volume_labels` (:gh:`11289` by :newcontrib:`Mauricio Cespedes Tenorio`)
• Fix bug in documentation of :func:`mne.channels.make_dig_montage` (:gh:`11235` by :newcontrib:`Daniel Hasegan`)
• Add support for bad channel handling in :func:`mne.set_bipolar_reference` (:gh:`11245` by `Moritz Gerster`_, :newcontrib:`Dinara Issagaliyeva`, :newcontrib:`Jennifer Behnke`, :newcontrib:`Hakimeh Aslsardroud`, and :newcontrib:`Pavel Navratil`)
• Fix X coordinates of ear_left and ear_right in head outlines dict (:gh:`11255` by :newcontrib:`Tom Ma`)
• Add type checking for tmin and tmax arguments for crop (:gh:`11263` by :newcontrib:`Carlos de la Torre-Ortiz`).
• Fix bug where trying to setup projection without an EEG average reference projector would fail (:gh:`11351` by :newcontrib:`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) (:gh:`11244` by `Eric Larson`_)
• Fix bug in automatic MESA detection for disabling advanced 3D options (:gh:`11271` by `Eric Larson`_)
• Fix bug in :func:`mne.head_to_mri` when unscale=True (:gh:`11303` by `Eric Larson`_)
• Fix bug in :meth:`set_montage('mgh60') <mne.io.Raw.set_montage>` and related functions where the 'mgh60' sensor positions were incorrectly ordered (:gh:`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 (:gh:`11248` by `Daniel McCloy`_)
• Fix bug in the :func:`~mne.viz.plot_evoked_topo` and :meth:`~mne.Evoked.plot_topo`, where legend colors where shown incorrectly on newer matplotlib versions (:gh:`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 :func:`~mne.io.read_raw_eeglab` and :func:`~mne.read_epochs_eeglab` to control in what units EEGLAB channel positions are read. The default is millimeters, 'mm' (:gh:`11283` by `Mikołaj Magnuski`_)
• Fix bug where computing PSD with welch's method with more jobs than channels would fail (:gh:`11298` by `Mathieu Scheltienne`_)
• Fix bug where the default FFT length changed for spectrum plots (:gh:`11345` by `Daniel McCloy`_)
• Fix bug with :func:`mne.decoding.cross_val_multiscore` where progress bars were not displayed correctly (:gh:`11311` by `Eric Larson`_)
• Fix channel selection edge-cases in ~mne.preprocessing.ICA.find_bads_muscle (:gh:`11300` by `Mathieu Scheltienne`_)
• Fix bug with :func:`mne.io.read_raw_curry` where a dot in the parent folders prevented files from being read (:gh:`11340` by `Eric Larson`_)
• Fix bug with :class:`mne.Report` with replace=True where the wrong content was replaced and section was not respected (:gh:`11318`, :gh:`11346` by `Eric Larson`_)
• Fix bug with unit conversion when setting reference MEG as the channel type in :meth:`mne.io.Raw.set_channel_types` and related methods (:gh:`11344` by `Eric Larson`_)
• Fix bug where reference MEG channels could not be plotted using :func:`mne.viz.plot_epochs_image` (:gh:`11344` by `Eric Larson`_)
• Fix bug where image_format='gif' was errantly documented as being supported by :class:`mne.Report`, it is now only supported in :meth:`mne.Report.add_image` (:gh:`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. (:gh:`11293` by `Daniel McCloy`_)
• Fix :meth:`mne.Epochs.plot_image` and :func:`mne.viz.plot_epochs_image` when using EMG signals (:gh:`11322` by `Alex Gramfort`_)
• Fix selection of ICA components in :func:`mne.viz.plot_ica_components` and :meth:`mne.preprocessing.ICA.plot_components` (:gh:`11369` by `Mathieu Scheltienne`_)
• Fix bug where a Freesurfer reconstruction run with both a T1 and a T2 caused :class:`mne.viz.Brain` not to initialize pial surfaces properly (:gh:`11361` by `Alex Rockhill`_)

API changes

• In :func:`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 :func:`~scipy.signal.windows.dpss` function are also exposed: sym (for choosing symmetric vs. periodic windows) and norm (window normalization method). (:gh:`11293` by `Daniel McCloy`_)
• In :meth:`mne.decoding.CSP.plot_patterns`, :meth:`mne.decoding.CSP.plot_filters`, :meth:`mne.preprocessing.ICA.plot_components`, and :func:`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 (:gh:`11371` by `Daniel McCloy`_)
• In :meth:`mne.decoding.CSP.plot_patterns` and :meth:`mne.decoding.CSP.plot_filters` the title parameter is deprecated and will be removed in version 1.4 (:gh:`11371` by `Daniel McCloy`_)
• The APIs of :meth:`mne.preprocessing.ICA.plot_components` and :func:`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 (:gh:`11371` by `Daniel McCloy`_)
• The APIs of :meth:`mne.decoding.CSP.plot_patterns` and :meth:`mne.decoding.CSP.plot_filters` gained new parameters extrapolate, border, cnorm, axes, nrows, ncols, for consistency with other topomap-plotting functions and methods (:gh:`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+