v1.6.rst

Version 1.6.0 (2023-11-20)

Enhancements

• Add support for Neuralynx data files with :func:`mne.io.read_raw_neuralynx` (:gh:`11969` by :newcontrib:`Kristijan Armeni` and :newcontrib:`Ivan Skelin`)
• Improve tests for saving splits with :class:`mne.Epochs` (:gh:`11884` by `Dmitrii Altukhov`_)
• Added functionality for linking interactive figures together, such that changing one figure will affect another, see :ref:`tut-ui-events` and :mod:`mne.viz.ui_events`. Current figures implementing UI events are :func:`mne.viz.plot_topomap` and :func:`mne.viz.plot_source_estimates` (:gh:`11685` :gh:`11891` by `Marijn van Vliet`_)
• HTML anchors for :class:`mne.Report` now reflect the section-title of the report items rather than using a global incrementor global-N (:gh:`11890` by `Eric Larson`_)
• Added public :func:`mne.io.write_info` to complement :func:`mne.io.read_info` (:gh:`11918` by `Eric Larson`_)
• Added option remove_dc to to :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>`, to allow skipping DC removal when computing Welch or multitaper spectra (:gh:`11769` by `Nikolai Chapochnikov`_)
• Add the possibility to provide a float between 0 and 1 as n_grad, n_mag and n_eeg in ~mne.compute_proj_raw, ~mne.compute_proj_epochs and ~mne.compute_proj_evoked to select the number of vectors based on the cumulative explained variance (:gh:`11919` by `Mathieu Scheltienne`_)
• Add extracting all time courses in a label using :func:`mne.extract_label_time_course` without applying an aggregation function (like mean) (:gh:`12001` by `Hamza Abdelhedi`_)
• Added support for Artinis fNIRS data files to :func:`mne.io.read_raw_snirf` (:gh:`11926` by `Robert Luke`_)
• Add helpful error messages when using methods on empty :class:`mne.Epochs`-objects (:gh:`11306` by `Martin Schulz`_)
• Add support for passing a :class:`python:dict` as sensor_color to specify per-channel-type colors in :func:`mne.viz.plot_alignment` (:gh:`12067` by `Eric Larson`_)
• Add inferring EEGLAB files' montage unit automatically based on estimated head radius using :func:`read_raw_eeglab(..., montage_units="auto") <mne.io.read_raw_eeglab>` (:gh:`11925` by `Jack Zhang`_, :gh:`11951` by `Eric Larson`_)
• Add :class:`~mne.time_frequency.EpochsSpectrumArray` and :class:`~mne.time_frequency.SpectrumArray` to support creating power spectra from :class:`NumPy array <numpy.ndarray>` data (:gh:`11803` by `Alex Rockhill`_)
• Add support for writing forward solutions to HDF5 and convenience function :meth:`mne.Forward.save` (:gh:`12036` by `Eric Larson`_)
• Refactored internals of :func:`mne.read_annotations` (:gh:`11964` by `Paul Roujansky`_)
• Add support for drawing MEG sensors in :ref:`mne coreg` (:gh:`12098` by `Eric Larson`_)
• Improve string representation of :class:`mne.Covariance` (:gh:`12181` by `Eric Larson`_)
• Add check_version=True to :ref:`mne sys_info` to check for a new release on GitHub (:gh:`12146` by `Eric Larson`_)
• Bad channels are now colored gray in addition to being dashed when spatial colors are used in :func:`mne.viz.plot_evoked` and related functions (:gh:`12142` by `Eric Larson`_)
• By default MNE-Python creates matplotlib figures with layout='constrained' rather than the default layout='tight' (:gh:`12050`, :gh:`12103` by `Mathieu Scheltienne`_ and `Eric Larson`_)
• Enhance :func:`~mne.viz.plot_evoked_field` with a GUI that has controls for time, colormap, and contour lines (:gh:`11942` by `Marijn van Vliet`_)
• Add :class:`mne.viz.ui_events.UIEvent` linking for interactive colorbars, allowing users to link figures and change the colormap and limits interactively. This supports :func:`~mne.viz.plot_evoked_topomap`, :func:`~mne.viz.plot_ica_components`, :func:`~mne.viz.plot_tfr_topomap`, :func:`~mne.viz.plot_projs_topomap`, :meth:`~mne.Evoked.plot_image`, and :meth:`~mne.Epochs.plot_image` (:gh:`12057` by `Santeri Ruuskanen`_)
• Add example KIT phantom dataset in :func:`mne.datasets.phantom_kit.data_path` and :ref:`tut-phantom-kit` (:gh:`12105` by `Judy D Zhu`_ and `Eric Larson`_)
• :func:`~mne.epochs.make_metadata` now accepts tmin=None and tmax=None, which will bound the time window used for metadata generation by event names (instead of a fixed time). That way, you can now for example generate metadata spanning from one cue or fixation cross to the next, even if trial durations vary throughout the recording (:gh:`12118` by `Richard Höchenberger`_)
• Add support for passing multiple labels to :func:`mne.minimum_norm.source_induced_power` (:gh:`12026` by `Erica Peterson`_, `Eric Larson`_, and `Daniel McCloy`_ )
• Added documentation to :meth:`mne.io.Raw.set_montage` and :func:`mne.add_reference_channels` to specify that montages should be set after adding reference channels (:gh:`12160` by `Jacob Woessner`_)
• Add argument splash to the function using the qt browser backend to allow enabling/disabling the splash screen (:gh:`12185` by `Mathieu Scheltienne`_)
• :class:`~mne.preprocessing.ICA`'s HTML representation (displayed in Jupyter notebooks and :class:`mne.Report`) now includes all optional fit parameters (e.g., max. number of iterations) (:gh:`12194`, by `Richard Höchenberger`_)

Bugs

• Fix bug where :func:`mne.io.read_raw_gdf` would fail due to improper usage of np.clip (:gh:`12168` by :newcontrib:`Rasmus Aagaard`)
• Fix bugs with :func:`mne.preprocessing.realign_raw` where the start of other was incorrectly cropped; and onsets and durations in other.annotations were left unsynced with the resampled data (:gh:`11950` by :newcontrib:`Qian Chu`)
• Fix bug where encoding argument was ignored when reading annotations from an EDF file (:gh:`11958` by :newcontrib:`Andrew Gilbert`)
• Mark tests test_adjacency_matches_ft and test_fetch_uncompressed_file as network tests (:gh:`12041` by :newcontrib:`Maksym Balatsko`)
• Fix bug with :func:`mne.channels.read_ch_adjacency` (:gh:`11608` by :newcontrib:`Ivan Zubarev`)
• Fix bug where epochs.get_data(..., scalings=...) would errantly modify the preloaded data (:gh:`12121` by :newcontrib:`Pablo Mainar` and `Eric Larson`_)
• Fix bugs with saving splits for :class:`~mne.Epochs` (:gh:`11876` by `Dmitrii Altukhov`_)
• Fix bug with multi-plot 3D rendering where only one plot was updated (:gh:`11896` by `Eric Larson`_)
• Fix bug where verbose level was not respected inside parallel jobs (:gh:`12154` by `Eric Larson`_)
• Fix bug where subject birthdays were not correctly read by :func:`mne.io.read_raw_snirf` (:gh:`11912` by `Eric Larson`_)
• Fix bug where warnings were emitted when computing spectra for channels marked as bad (:gh:`12186` by `Eric Larson`_)
• Fix bug with :func:`mne.chpi.compute_head_pos` for CTF data where digitization points were modified in-place, producing an incorrect result during a save-load round-trip (:gh:`11934` by `Eric Larson`_)
• Fix bug where non-compliant stimulus data streams were not ignored by :func:`mne.io.read_raw_snirf` (:gh:`11915` by `Johann Benerradi`_)
• Fix bug with pca=False in :func:`mne.minimum_norm.compute_source_psd` (:gh:`11927` by `Alex Gramfort`_)
• Fix bug with notebooks when using PyVista 0.42 by implementing trame backend support (:gh:`11956` by `Eric Larson`_)
• Removed preload parameter from :func:`mne.io.read_raw_eyelink`, because data are always preloaded no matter what preload is set to (:gh:`11910` by `Scott Huberty`_)
• Fix bug with :meth:`mne.viz.Brain.get_view` where calling :meth:`~mne.viz.Brain.show_view` with returned parameters would change the view (:gh:`12000` by `Eric Larson`_)
• Fix bug with :meth:`mne.viz.Brain.show_view` where distance=None would change the view distance (:gh:`12000` by `Eric Larson`_)
• Fix bug with :meth:`~mne.viz.Brain.add_annotation` when reading an annotation from a file with both hemispheres shown (:gh:`11946` by `Marijn van Vliet`_)
• Fix bug with reported component number and errant reporting of PCA explained variance as ICA explained variance in :meth:`mne.Report.add_ica` (:gh:`12155`, :gh:`12167` by `Eric Larson`_ and `Richard Höchenberger`_)
• Fix bug with axis clip box boundaries in :func:`mne.viz.plot_evoked_topo` and related functions (:gh:`11999` by `Eric Larson`_)
• Fix bug with subject_info when loading data from and exporting to EDF file (:gh:`11952` by `Paul Roujansky`_)
• Fix bug where :class:`mne.Info` HTML representations listed all channel counts instead of good channel counts under the heading "Good channels" (:gh:`12145` by `Eric Larson`_)
• Fix rendering glitches when plotting Neuromag/TRIUX sensors in :func:`mne.viz.plot_alignment` and related functions (:gh:`12098` by `Eric Larson`_)
• Fix bug with delayed checking of :class:`info["bads"] <mne.Info>` (:gh:`12038` by `Eric Larson`_)
• Fix bug with :ref:`mne coreg` where points inside the head surface were not shown (:gh:`12147`, :gh:`12164` by `Eric Larson`_)
• Fix bug with :func:`mne.viz.plot_alignment` where sensor_colors were not handled properly on a per-channel-type basis (:gh:`12067` by `Eric Larson`_)
• Fix handling of channel information in annotations when loading data from and exporting to EDF file (:gh:`11960` :gh:`12017` :gh:`12044` by `Paul Roujansky`_)
• Add missing overwrite and verbose parameters to :meth:`Transform.save() <mne.transforms.Transform.save>` (:gh:`12004` by `Marijn van Vliet`_)
• Fix parsing of eye-link :class:`~mne.Annotations` when apply_offsets=False is provided to :func:`~mne.io.read_raw_eyelink` (:gh:`12003` by `Mathieu Scheltienne`_)
• Correctly prune channel-specific :class:`~mne.Annotations` when creating :class:`~mne.Epochs` without the channel(s) included in the channel specific annotations (:gh:`12010` by `Mathieu Scheltienne`_)
• Fix :func:`~mne.viz.plot_volume_source_estimates` with :class:`~mne.VolSourceEstimate` which include a list of vertices (:gh:`12025` by `Mathieu Scheltienne`_)
• Add support for non-ASCII characters in Annotations, Evoked comments, etc when saving to FIFF format (:gh:`12080` by `Daniel McCloy`_)
• Correctly handle passing "eyegaze" or "pupil" to :meth:`mne.io.Raw.pick` (:gh:`12019` by `Scott Huberty`_)
• Fix bug with :func:`mne.time_frequency.Spectrum.plot` and related functions where bad channels were not marked (:gh:`12142` by `Eric Larson`_)
• Fix bug with :func:`~mne.viz.plot_raw` where changing MNE_BROWSER_BACKEND via :func:`~mne.set_config` would have no effect within a Python session (:gh:`12078` by `Santeri Ruuskanen`_)
• Improve handling of method argument in the channel interpolation function to support :class:`str` and raise helpful error messages (:gh:`12113` by `Mathieu Scheltienne`_)
• Fix combination of DIN event channels into a single synthetic trigger channel STI 014 by the MFF reader of :func:`mne.io.read_raw_egi` (:gh:`12122` by `Mathieu Scheltienne`_)
• Fix bug with :func:`mne.io.read_raw_eeglab` and :func:`mne.read_epochs_eeglab` where automatic fiducial detection would fail for certain files (:gh:`12165` by `Clemens Brunner`_)
• Fix concatenation of raws with np.nan in the device to head transformation (:gh:`12198` by `Mathieu Scheltienne`_)
• Fix bug with :func:`mne.viz.plot_compare_evokeds` where the title was not displayed when axes='topo' (:gh:`12192` by `Jacob Woessner`_)
• Fix bug with :func:`mne.io.read_raw_cnt` where the bad channels were not properly read (:gh:`12189` by `Jacob Woessner`_)
• Fix bug where iterating over :class:`~mne.io.Raw` would result in an error (:gh:`12205` by `Clemens Brunner`_)

API changes

• The default for :meth:`mne.Epochs.get_data` of copy=False will change to copy=True in 1.7. Set it explicitly to avoid a warning (:gh:`12121` by :newcontrib:`Pablo Mainar` and `Eric Larson`_)
• mne.preprocessing.apply_maxfilter and mne maxfilter have been deprecated and will be removed in 1.7. Use :func:`mne.preprocessing.maxwell_filter` (see :ref:`this tutorial <tut-artifact-sss>`) in Python or the command-line utility from MEGIN maxfilter and :func:`mne.bem.fit_sphere_to_headshape` instead (:gh:`11938` by `Eric Larson`_)
• :func:`mne.io.kit.read_mrk` reading pickled files is deprecated using something like np.savetxt(fid, pts, delimiter="\t", newline="\n") to save your points instead (:gh:`11937` by `Eric Larson`_)
• Replace legacy inst.pick_channels and inst.pick_types with inst.pick (where inst is an instance of :class:`~mne.io.Raw`, :class:`~mne.Epochs`, or :class:`~mne.Evoked`) wherever possible (:gh:`11907` by `Clemens Brunner`_)
• The reset_camera parameter has been removed in favor of distance="auto" in :func:`mne.viz.set_3d_view`, :meth:`mne.viz.Brain.show_view`, and related functions (:gh:`12000` by `Eric Larson`_)
• Several unused parameters from :func:`mne.gui.coregistration` are now deprecated: tabbed, split, scrollable, head_inside, guess_mri_subject, scale, and advanced_rendering. All arguments are also now keyword-only. (:gh:`12147` by `Eric Larson`_)

Authors

• Adam Li
• Alex Rockhill
• Alexandre Gramfort
• Ana Radanovic
• Andy Gilbert+
• Clemens Brunner
• Daniel McCloy
• Denis A. Engemann
• Dimitri Papadopoulos Orfanos
• Dmitrii Altukhov
• Dominik Welke
• Eric Larson
• Erica Peterson
• Gonzalo Reina
• Hamza Abdelhedi
• Ivan Skelin+
• Ivan Zubarev+
• Jack Zhang
• Jacob Woessner
• Johann Benerradi
• John Veillette
• Judy D Zhu
• Kristijan Armeni+
• Mainak Jas
• Maksym Balatsko+
• Marijn van Vliet
• Martin Schulz
• Mathieu Scheltienne
• Nikolai Chapochnikov
• Pablo Mainar+
• Paul Roujansky
• Qian Chu+
• Rasmus Aagaard+
• Richard Höchenberger
• Rob Luke
• Santeri Ruuskanen
• Scott Huberty
• Stefan Appelhoff