v0.21.rst

Version 0.21 (2020-09-21)

Enhancements

• Modified :meth:`mne.Epochs.pick_types` to remove dropped channel types from reject and flat dictionaries by new contributor |Rahul Nadkarni|_
• Add function :func:`mne.preprocessing.regress_artifact` to remove artifacts using linear regression by new contributor |Kyle Mathewson|_ and `Eric Larson`_
• Add sources and detectors options for fNIRS use of :meth:`mne.viz.plot_alignment` allowing plotting of optode locations in addition to channel midpoint channels and path between fNIRS optodes by new contributor |Kyle Mathewson|_
• BrainVision data format files are now parsed for EEG impedance values in :func:`mne.io.read_raw_brainvision` and provided as a .impedances attribute of raw by new contributor |Jan Sedivy|_ and `Stefan Appelhoff`_
• Add function :func:`mne.channels.combine_channels` to combine channels from Raw, Epochs, or Evoked according to ROIs (combinations including mean, median, or standard deviation; can also use a callable) by new contributor |Johann Benerradi|_
• Improved documentation building instructions and execution on Windows by new contributor |Martin Schulz|_, `Evgenii Kalenkovich`_, and `Eric Larson`_
• Speed up reading of annotations in EDF+ files by new contributor |Jeroen Van Der Donckt|_
• Add head to mri and mri to voxel space transform details to :ref:`tut-source-alignment` tutorial, by `Alex Rockhill`_
• Improve memory efficiency of :func:`mne.concatenate_epochs` by `Eric Larson`_
• Allow picking channels in raw instances (e.g., :meth:`mne.io.Raw.pick_types`) without preloading data, by `Eric Larson`_
• :meth:`mne.preprocessing.ICA.plot_sources` now plots annotation markers similar to :meth:`mne.io.Raw.plot` by `Luke Bloy`_
• Add support for scalar multiplication and division of :class:`mne.time_frequency.AverageTFR` instances by `Luke Bloy`_
• Add support for signals in mV for :func:`mne.io.read_raw_brainvision` by `Clemens Brunner`_
• :meth:`mne.Epochs.plot_psd_topomap` and :func:`mne.viz.plot_epochs_psd_topomap` now allow joint colorbar limits across subplots, by `Daniel McCloy`_.
• Add support for using loose-orientation surface priors with free-orientation volume priors in mixed source space inverses by `Eric Larson`_
• Add :class:`mne.MixedVectorSourceEstimate` for vector source estimates for mixed source spaces, by `Eric Larson`_
• Add mixed and volumetric source estimate plotting using volumetric ray-casting to :meth:`mne.MixedSourceEstimate.plot` and :meth:`mne.VolSourceEstimate.plot_3d` by `Eric Larson`_
• Add :meth:`mne.MixedSourceEstimate.surface` and :meth:`mne.MixedSourceEstimate.volume` methods to allow surface and volume extraction by `Eric Larson`_
• Add :meth:`mne.VectorSourceEstimate.project` to project vector source estimates onto the direction of maximum source power by `Eric Larson`_
• Add support to :func:`mne.extract_label_time_course` for vector-valued and volumetric source estimates by `Eric Larson`_
• Add method :meth:`mne.VolSourceEstimate.in_label` by `Eric Larson`_
• Add support for mixed source spaces to :func:`mne.compute_source_morph` by `Eric Larson`_
• Add support for volume and mixed source spaces to :func:`mne.stats.summarize_clusters_stc` by `Eric Larson`_
• Add support for omitting the SDR step in volumetric morphing by passing n_iter_sdr=() to mne.compute_source_morph by `Eric Larson`_
• Add single_volume argument to :func:`mne.setup_volume_source_space` to facilitate creating source spaces with many volumes (e.g., all subvolumes of aseg.mgz) by `Eric Larson`_
• Add support for passing a string argument to bg_img in mne.viz.plot_volume_source_estimates by `Eric Larson`_
• Add support for providing the destination surface source space in the src_to argument of :func:`mne.compute_source_morph` by `Eric Larson`_
• Add explained variance logging to :func:`mne.inverse_sparse.mixed_norm`, :func:`mne.inverse_sparse.gamma_map`, and :func:`mne.beamformer.rap_music` by `Eric Larson`_
• Add tol_kind option to :func:`mne.compute_rank` by `Eric Larson`_
• Allow resampling raw data with :func:`mne.io.Raw.resample` without preloading data, by `Eric Larson`_
• Allow using pick_ori='vector' with a fixed-orientation inverse to facilitate visualization with :func:`mne.viz.plot_vector_source_estimates` by `Eric Larson`_
• :func:`mne.viz.plot_dipole_locations` and :meth:`mne.Dipole.plot_locations` gained a title argument to specify a custom figure title in orthoview mode by `Richard Höchenberger`_
• Add orientations projected onto the MRI slices in :func:`mne.viz.plot_dipole_locations` in 'orthoview' mode by `Eric Larson`_
• Add temporal derivative distribution repair (TDDR) :func:`mne.preprocessing.nirs.temporal_derivative_distribution_repair` with shortened alias mne.preprocessing.nirs.tddr by `Robert Luke`_
• Add :func:`mne.read_freesurfer_lut` to make it easier to work with volume atlases by `Eric Larson`_
• Add support for overlap-add processing when method='spectrum_fit' in :func:`mne.io.Raw.notch_filter` by `Eric Larson`_
• Add functionality to interpolate bad NIRS channels by `Robert Luke`_
• Add ability to interpolate EEG channels using minimum-norm projection in :meth:`mne.io.Raw.interpolate_bads` and related functions with method=dict(eeg='MNE') by `Eric Larson`_
• Added ability of :func:`mne.io.read_raw_nirx` to open data by passing path to header file `Robert Luke`_
• Add :meth:`mne.channels.DigMontage.rename_channels` to allow renaming montage channels by `Eric Larson`_
• Document :meth:`mne.channels.compute_native_head_t` to allow computing the native-to-head transformation that will be applied when doing :meth:`raw.set_montage <mne.io.Raw.set_montage>` and related functions by `Eric Larson`_
• Add support to in :meth:`mne.io.Raw.plot` for passing clipping as a float to clip to a proportion of the dedicated channel range by `Eric Larson`_
• Add function :func:`mne.preprocessing.annotate_muscle_zscore` to annotate periods with muscle artifacts. by `Adonay Nunes`_
• Add :func:`mne.stats.ttest_ind_no_p` to mirror :func:`mne.stats.ttest_1samp_no_p` with hat correction by `Eric Larson`_
• Add mne.stats.combine_adjacency to combine adjacency matrices for independent data dimensions to enable things like spatio-temporal-time-frequency clustering in mne.stats.permutation_cluster_test by `Eric Larson`_
• Speed up raw data reading without preload in :func:`mne.io.read_raw_nirx` by `Eric Larson`_
• Speed up :meth:`mne.Epochs.copy` and :meth:`mne.Epochs.__getitem__` by avoiding copying immutable attributes by `Eric Larson`_
• Speed up and reduce memory usage of :meth:`mne.SourceEstimate.plot` and related functions/methods when show_traces=True by `Eric Larson`_
• Reduce memory usage of ~mne.io.Raw.plot_psd, mne.time_frequency.psd_welch, and ~mne.time_frequency.psd_array_welch for long segments of data by `Eric Larson`_
• Support for saving movies of source time courses (STCs) with brain.save_movie method and from graphical user interface by `Guillaume Favelier`_
• Add mri and show_orientation arguments to :func:`mne.viz.plot_bem` by `Eric Larson`_
• Add :func:`mne.viz.centers_to_edges` to help when using :meth:`matplotlib.axes.Axes.pcolormesh` with flat shading by `Eric Larson`_
• Add on_missing='raise' to :meth:`mne.io.Raw.set_montage` and related functions to allow ignoring of missing electrode coordinates by `Adam Li`_
• Add on_missing='raise' to :func:`mne.viz.plot_events` to allow ignoring missing events when passing event_id by `Eric Larson`_
• Add REST EEG infinity reference scheme to :meth:`mne.io.Raw.set_eeg_reference` and related functions by `Eric Larson`_
• Add better sanity checking of max_pca_components and n_components to provide more informative error messages for :class:`mne.preprocessing.ICA` by `Eric Larson`_
• Add plot option to :meth:`mne.viz.plot_filter` allowing selection of which filter properties are plotted and added option for user to supply axes by `Robert Luke`_
• Add estimation method legend to :func:`mne.viz.plot_snr_estimate` by `Eric Larson`_
• Add support to mne.SourceSpaces.export_volume for mri_resolution='sparse' to color only the nearest-neighbor voxels instead of entire regions by `Eric Larson`_
• Add axes argument to :func:`mne.viz.plot_evoked_white`, :meth:`mne.Evoked.plot_white`, and :func:`mne.viz.plot_snr_estimate` by `Eric Larson`_
• Change default to surfaces='auto' from surfaces='head' to allow :func:`mne.viz.plot_alignment` to work when just passing a :class:`mne.Info` as plot_alignment(info) by `Eric Larson`_
• Add ECoG misc EDF dataset to the :ref:`tut-working-with-ecog` tutorial to show snapshots of time-frequency activity by `Adam Li`_
• Add :func:`mne.viz.set_3d_options` and MNE_3D_OPTION_ANTIALIAS environment variable to control full-scene antialiasing (FXAA) in 3D functions like :ref:`mne coreg`, :func:`mne.viz.plot_alignment`, and :func:`mne.viz.plot_source_estimates`; this can be useful on systems where FXAA does not work well, such as some with MESA software rendering, by `Eric Larson`_
• Add config variable MNE_TQDM to support explicitly setting the TQDM backend to use, for example tqdm or tqdm.auto (default) by `Eric Larson`_
• Add better support for reading corrupted FIF files in :func:`mne.io.read_raw_fif` by `Eric Larson`_
• BIDS conformity: When saving FIF files to disk and the files are split into parts, the split_naming='bids' parameter now uses a "_split-%d" naming instead of the previous "_part-%d", by `Stefan Appelhoff`_
• Add support for whitening and multiple channel types in :func:`mne.beamformer.make_dics` by `Marijn van Vliet`_
• Add better error message when trying to save incompatible ~mne.Evoked objects to the same file by `Eric Larson`_
• Add support for loading complex numbers from mat files by `Thomas Hartmann`_
• Add generic reader function :func:`mne.io.read_raw` that loads files based on their extensions (it wraps the underlying specific read_raw_xxx functions) by `Clemens Brunner`_
• Add automatic T3 magnetometer detection and application of :meth:`mne.io.Raw.fix_mag_coil_types` to :func:`mne.preprocessing.maxwell_filter` by `Eric Larson`_
• Add extended SSS (eSSS) support to :func:`mne.preprocessing.maxwell_filter` by `Eric Larson`_
• Add 'auto' option to :meth:`mne.preprocessing.ICA.find_bads_ecg` to automatically determine the threshold for CTPS method by `Yu-Han Luo`_
• Add a notebook 3d backend for visualization in jupyter notebook with :func:`mne.viz.set_3d_backend` by `Guillaume Favelier`_
• Add support for reading and writing surfaces in Wavefront .obj format to the :func:`mne.read_surface` and :func:`mne.write_surface` by `Marijn van Vliet`_
• Add tutorial on how to manually fix BEM meshes in Blender by `Marijn van Vliet`_ and `Ezequiel Mikulan`_
• :func:`mne.write_evokeds` will now accept :class:`mne.Evoked` objects with differing channel orders in info['bads'], which would previously raise an exception by `Richard Höchenberger`_
• Add support for reading channel names (e.g., for Ricoh data) to :func:`mne.io.read_raw_kit` by `Alex Gramfort`_ and `Eric Larson`_
• The reject_tmin and reject_tmax parameters of :class:`mne.Epochs` are now taken into account when using the reject_by_annotation parameter by `Stefan Appelhoff`_
• :func:`mne.preprocessing.find_bad_channels_maxwell` now automatically applies a low-pass filter before running bad channel detection. This can be disabled, restoring previous behavior by `Richard Höchenberger`_
• Add proj='reconstruct' to :meth:`mne.Evoked.plot` and related functions to apply projectors and then undo the signal bias using field mapping by `Eric Larson`_
• Add writing BEM surfaces and solutions in H5 format in :func:`mne.write_bem_surfaces` and :func:`mne.write_bem_solution` by `Eric Larson`_
• When picking a subset of channels, or when dropping channels from ~mne.io.Raw, ~mne.Epochs, or ~mne.Evoked, projectors that can only be applied to the removed channels will now be dropped automatically by `Richard Höchenberger`_
• :class:`mne.Report` now can add topomaps of SSP projectors to the generated report. This behavior can be toggled via the new projs argument by `Richard Höchenberger`_
• When passing a list of ~mne.Evoked objects to ~mne.viz.plot_compare_evokeds, each evoked's .comment attribute will be used to label the trace. If .comment is empty, a 1-based index is assigned as the label by `Richard Höchenberger`_
• Speed up :func:`mne.stats.summarize_clusters_stc` using Numba by `Yu-Han Luo`_
• Add reject_by_annotation=True to :func:`mne.make_fixed_length_epochs` and :meth:`mne.preprocessing.ICA.plot_properties` to reject bad data segments based on annotation by `Yu-Han Luo`_
• ~mne.Report.parse_folder now accepts a path-like folder name (it used to work with strings only) by `Alex Gramfort`_
• Add component_order parameter to :class:`mne.decoding.CSP` which allows switching between mutual_info (default) and alternate (a simpler and frequently used option) by `Martin Billinger`_ and `Clemens Brunner`_
• Add memory size information to the repr of :class:`mne.SourceSpaces` and :class:`mne.SourceEstimate` and related classes by `Eric Larson`_
• Add reader for Persyst (.lay + .dat format) data in :func:`mne.io.read_raw_persyst` by `Adam Li`_
• Use PyVista as the default backend for 3D visualization instead of Mayavi by `Guillaume Favelier`_
• Add reader for SNIRF NIRS data in :func:`mne.io.read_raw_snirf` by `Robert Luke`_
• ~mne.Evoked has gained tmin and tmax attributes for more consistency with ~mne.Epochs by `Richard Höchenberger`_

Bugs

• Fix bug for writing and reading complex evoked data modifying :func:`mne.write_evokeds` and :func:`mne.read_evokeds` by new contributor |Lau Møller Andersen|_
• Fix bug by adding error message when trying to save complex stc data in a non.-h5 format :meth:`mne.VolSourceEstimate.save` by new contributor |Lau Møller Andersen|_
• Fix bug with logging in :meth:`mne.io.Raw.set_eeg_reference` and related functions by new contributor |Simeon Wong|_
• Fix bug with :func:`mne.io.read_raw_gdf` where birthdays were not parsed properly, leading to an error by new contributor |Svea Marie Meyer|_
• Fix bug with :func:`mne.io.read_raw_edf` where recording ID was not read properly for non-ASCII characters by new contributor |Lx37|_
• Fix bug in :func:`mne.set_eeg_reference` and related functions to set info['custom_ref_applied'] to True for 'ecog' and 'seeg' channels in addition to 'eeg' by new contributor |Liberty Hamilton|_
• Fix bug with :func:`mne.chpi.compute_chpi_amplitudes` and :func:`mne.chpi.filter_chpi` to optimize time window length by new contributor |Steven Bierer|_
• Fix bug with :func:`mne.preprocessing.ICA.find_bads_eog` when more than one EOG components are present by `Christian O'Reilly`_
• Fix bug with non-preloaded data when using raw.apply_proj().load_data().get_data() where projectors were not applied by `Eric Larson`_
• Fix bug to permit :meth:`stc.project('nn', src) <mne.VectorSourceEstimate.project>` to be applied after stc was restricted to an :class:`mne.Label` by `Luke Bloy`_
• Fix bug with :func:`mne.io.Raw.set_meas_date` to support setting meas_date to None, by `Luke Bloy`_
• Fix bug with :func:`mne.setup_volume_source_space` when volume_label was supplied where voxels slightly (in a worst case, about 37% times pos in distance) outside the voxel-grid-based bounds of regions were errantly included, by `Eric Larson`_
• Fix bug with :ref:`mne coreg` where reverse scalings were applied to src[0]['src_mri_t'] for volume source spaces, so morphing and plotting did not work correctly by `Eric Larson`_
• Fix bug with :func:`mne.io.read_raw_ctf` when reference magnetometers have the compensation grade marked by `Eric Larson`_
• Fix bug with mne.SourceSpaces.export_volume with use_lut=False where no values were written by `Eric Larson`_
• Fix bug with :func:`mne.preprocessing.annotate_movement` where bad data segments, specified in raw.annotations, would be handled incorrectly by `Luke Bloy`_
• Fix bug with :func:`mne.compute_source_morph` when more than one volume source space was present (e.g., when using labels) where only the first label would be interpolated when mri_resolution=True by `Eric Larson`_
• Fix bug with :func:`mne.compute_source_morph` when morphing to a volume source space when src_to is used and the destination subject is not fsaverage by `Eric Larson`_
• Fix bug with :func:`mne.compute_source_morph` where outermost voxels in the destination source space could be errantly omitted by `Eric Larson`_
• Fix bug with :func:`mne.compute_source_morph` where complex data was cast to real when doing a volumetric morph by `Eric Larson`_
• Fix bug with :func:`mne.minimum_norm.compute_source_psd_epochs` and :func:`mne.minimum_norm.source_band_induced_power` raised errors when method='eLORETA' by `Eric Larson`_
• Fix bug with :func:`mne.minimum_norm.apply_inverse` where the explained variance did not work for complex data by `Eric Larson`_
• Fix bug with :func:`mne.preprocessing.compute_current_source_density` where values were not properly computed; maps should now be more focal, by `Alex Rockhill`_ and `Eric Larson`_
• Fix bug with :func:`mne.combine_evoked` where equal-weighted averages were wrongly computed as equal-weighted sums, by `Daniel McCloy`_
• Fix bug with :meth:`mne.channels.DigMontage.plot` when reference channels with no defined position are present, by `Eric Larson`_
• Fix bug with :func:`mne.channels.read_custom_montage` where "headshape" points in SFP format were not read properly, by `Eric Larson`_
• Fix bug with setting HTML classes when using mne.Report.add_bem_to_section by `Eric Larson`_
• Fix bug with convex-hull based MEG helmet creation where the face area could be covered up, by `Eric Larson`_
• Fix bug with :func:`mne.inverse_sparse.mixed_norm` and :func:`mne.inverse_sparse.gamma_map` with return_as_dipoles=True and :func:`mne.beamformer.rap_music` where dip.gof was the same for all dipoles. GOF values / explained variance across all dipoles now gets split among the dipoles using SVD of the lead fields. To get the total GOF, sum(dip.gof for dip in dipoles) can be used, by `Eric Larson`_
• Fix bug with :func:`mne.inverse_sparse.gamma_map` where output data was not assigned properly when using a free-orientation forward and xyz_same_gamma=False by `Eric Larson`_
• Fix to enable interactive plotting with no colorbar with :func:`mne.viz.plot_evoked_topomap` by `Daniel McCloy`_
• Fix plotting with :func:`mne.viz.plot_evoked_topomap` to pre-existing axes by `Daniel McCloy`_
• Fix bug with :func:`mne.viz.plot_vector_source_estimates` using the PyVista backend with time_viewer=True when updating the arrow colormaps by `Eric Larson`_
• Fix bug with :func:`mne.viz.plot_vector_source_estimates` where clim='auto' and clim=dict(..., kind='percent') did not take into account the magnitude of the activation, by `Eric Larson`_
• The default plotting mode for :func:`mne.io.Raw.plot` and :ref:`mne browse_raw` has been changed to clipping=3. to facilitate data analysis with large deflections, by `Eric Larson`_
• PSD plots will now show non-data channels (e.g., misc) if those channels are explicitly passed to picks, by `Daniel McCloy`_.
• Fix bug with :func:`mne.time_frequency.read_tfrs` where info['meas_date'] was not parsed correctly, by `Eric Larson`_
• Fix bug with :func:`mne.time_frequency.tfr_array_stockwell` where inputs were not properly validated by `Eric Larson`_
• Fix handling of NaN when using TFCE in clustering functions such as :func:`mne.stats.spatio_temporal_cluster_1samp_test` by `Eric Larson`_
• Fix handling of signs when using TFCE by `Eric Larson`_
• The :class:`mne.MixedSourceEstimate` class has been clarified to contain two cortical surface source spaces, plus at least one other source space. Creating source estimates in other orderings is not supported, by `Eric Larson`_
• Fix bug where :class:`VolSourceEstimate.vertices <mne.VolSourceEstimate>` was an instance of :class:`~numpy.ndarray` instead of :class:`python:list` of one :class:`~numpy.ndarray`, by `Eric Larson`_
• Fix default to be foreground=None in :func:`mne.viz.plot_source_estimates` to use white or black text based on the background color by `Eric Larson`_
• Fix bug with writing EGI and CTF mne.Info to H5 format, e.g., with mne.time_frequency.AverageTFR.save by `Eric Larson`_
• Fix bug with topomap outlines in :meth:`mne.time_frequency.AverageTFR.plot_joint` and :meth:`mne.time_frequency.AverageTFR.plot_topo` by `Eric Larson`_
• Fix bug with :func:`mne.io.Raw.plot` where toggling all projectors did not actually take effect by `Eric Larson`_
• Fix bug with :func:`mne.write_proj` where the number of columns was incorrectly written by `Eric Larson`_
• Fix bug with :func:`mne.read_epochs` when loading data in complex format with preload=False by `Eric Larson`_
• Fix bug with :meth:`mne.Epochs.save` where the file splitting calculations did not account for the sizes of non-data writes by `Eric Larson`_
• Fix bug with :class:`mne.Epochs` when metadata was not subselected properly when event_repeated='drop' by `Eric Larson`_
• Fix bug with :class:`mne.Epochs` where epochs.drop_log was a list of list of str rather than an immutable tuple of tuple of str (not meant to be changed by the user) by `Eric Larson`_
• Fix bug with :class:`mne.Report` where the BEM section could not be toggled by `Eric Larson`_
• Fix bug when using :meth:`mne.Epochs.crop` to exclude the baseline period would break :func:`mne.Epochs.save` / :func:`mne.read_epochs` round-trip by `Eric Larson`_
• Fix bug with mne.Epochs.subtract_evoked where using decimated epochs would lead to an error by `Eric Larson`_
• Fix bug with :func:`mne.viz.plot_bem` and :class:`mne.Report` when plotting BEM contours when MRIs are not in standard FreeSurfer orientation by `Eric Larson`_
• Fix bug with :func:`mne.minimum_norm.make_inverse_operator` where it would warn even when an explicit rank was used by `Eric Larson`_
• Fix bugs with :func:`mne.beamformer.make_lcmv` and :func:`mne.beamformer.make_dics` where:
  • Noise normalization factors weight_norm='unit-noise-gain' and weight_norm='nai' were computed incorrectly
  • pick_ori='max-power' computed the max-power orientation incorrectly
  • pick_ori='normal' did not compute power or noise normalization factors correctly
  • :func:`mne.beamformer.apply_lcmv_cov` did not apply whitening and projections properly
• Fix :ref:`mne setup_forward_model` to have it actually compute the BEM solution in addition to creating the BEM model by `Eric Larson`_
• Fix bug with :func:`mne.io.read_raw_edf` where null bytes were not properly handled, causing an error when opening a file by `Eric Larson`_
• Fix bug with :func:`mne.Report` where unicode characters were not rendered properly (encoding for HTML was not set) by `Eric Larson`_
• Fix bug with :func:`mne.preprocessing.nirs.scalp_coupling_index` where filter transition was incorrectly assigned by `Robert Luke`_
• Fix bug with :func:`mne.make_forward_dipole` where :func:`mne.write_forward_solution` could not be used by `Eric Larson`_
• Fix bug with :meth:`mne.io.Raw.plot` when scalings='auto' where bad data would prevent channel plotting by `Eric Larson`_
• Default border and extrapolate arguments for :func:`mne.Evoked.plot_topomap` and related functions were changed from 0. to 'mean' and 'box' to 'auto', respectively, to help more accurately reflect sensor geometries and boundary conditions. extrapolate='auto' uses extrapolate='local' for MEG data and extrapolate='head' otherwise, by `Eric Larson`_
• Fix bug that prevents n_jobs from being a NumPy integer type, by `Daniel McCloy`_.
• Fix bug with :func:`mne.epochs.average_movements` where epoch weights were computed using all basis vectors instead of the internal basis only by `Eric Larson`_
• Fix bug with :func:`mne.get_volume_labels_from_aseg` where the returned labels were alphabetical instead of reflecting their volumetric ID-based order by `Eric Larson`_
• Fix bug with :func:`mne.preprocessing.find_bad_channels_maxwell` where good data of exactly step duration would lead to an error by `Eric Larson`_
• Fix bug with :func:`mne.preprocessing.find_bad_channels_maxwell` where indices were not handled properly when MEG channels were not first in the raw instance, and logging messages incorrectly reported the interval used by `Eric Larson`_
• Make :func:`mne.set_config` accept path-like input values by `Richard Höchenberger`_
• Fix bug with :func:`mne.write_labels_to_annot` and :func:`mne.datasets.fetch_hcp_mmp_parcellation` where label name strings were not properly terminated, leading to problems loading in FreeSurfer by `Eric Larson`_
• Fix bug with :func:`mne.beamformer.make_dics` where complex conjugates were not applied properly by `Britta Westner`_ and `Eric Larson`_
• Fix bug with :func:`mne.bem.make_watershed_bem` where the RAS coordinates of watershed bem surfaces were not updated correctly from the volume file by `Yu-Han Luo`_
• Fix bug with :meth:`mne.io.Raw.get_channel_types` and related methods where the ordering of picks was not preserved, by `Eric Larson`_
• Fix bug with :meth:`mne.io.Raw.plot_psd` with average=False and multiple channel types where channel locations were not shown properly by `Eric Larson`_
• Fix bug with :func:`mne.viz.plot_sparse_source_estimates` when using 'sphere' mode by `Eric Larson`_ and `Guillaume Favelier`_
• Fix bug in FieldTrip reader functions when channels are missing in the info object by `Thomas Hartmann`_
• Throw proper error when trying to import FieldTrip Epochs data with non-uniform time for trials by `Thomas Hartmann`_
• Throw proper error when trying to import FieldTrip data saved by an old, incompatible version by `Thomas Hartmann`_
• Fix bug in :func:`mne.read_epochs_fieldtrip` when importing data without a trialinfo field by `Thomas Hartmann`_
• Fix bug in :meth:`mne.preprocessing.ICA.plot_properties` where time series plot doesn't start at the proper tmin by `Teon Brooks`_
• Fix bug with :meth:`mne.preprocessing.ICA.plot_properties` where a :class:`mne.io.Raw` object with annotations would lead to an error by `Yu-Han Luo`_
• Fix bug with :func:`mne.events_from_annotations(raw.annotations) <mne.events_from_annotations>` when orig_time of annotations is None and raw.first_time > 0, by `Alex Gramfort`_

API changes

• Python 3.5 is no longer supported, Python 3.6+ is required, by `Eric Larson`_

• adjacency has replaced connectivity in the names of:

  1. Arguments to clustering functions, such as mne.stats.permutation_cluster_test, and
  2. Function names for defining adjacency, such as mne.spatio_temporal_src_adjacency replacing mne.spatio_temporal_src_connectivity.

  The complete list of changed function names is:

  • mne.channels.find_ch_connectivity → ~mne.channels.find_ch_adjacency
  • mne.channels.read_ch_connectivity → ~mne.channels.read_ch_adjacency
  • mne.spatial_dist_connectivity → ~mne.spatial_dist_adjacency
  • mne.spatial_inter_hemi_connectivity → ~mne.spatial_inter_hemi_adjacency
  • mne.spatial_src_connectivity → ~mne.spatial_src_adjacency
  • mne.spatial_tris_connectivity → ~mne.spatial_tris_adjacency
  • mne.spatio_temporal_dist_connectivity → ~mne.spatio_temporal_dist_adjacency
  • mne.spatio_temporal_src_connectivity → ~mne.spatio_temporal_src_adjacency
  • mne.spatio_temporal_tris_connectivity → ~mne.spatio_temporal_tris_adjacency

  "connectivity" is now reserved for discussions of functional and effective connectivity of the brain, and "adjacency" for source or sensor neighbor definitions for cluster-based analyses, by `Eric Larson`_.

• The default for the standardize_names argument of :func:`mne.io.read_raw_kit` will change from True to False in 0.22, by `Eric Larson`_

• The normalize_fwd argument of :func:`mne.beamformer.make_dics` has been deprecated in favor of depth, by `Eric Larson`_

• The overwrite parameter of :func:`mne.write_bem_surfaces` and :func:`mne.write_bem_solution` defaults to True in 0.21 but will change to False in 0.22, by `Eric Larson`_

• Add n_cols parameter to :meth:`mne.preprocessing.ICA.plot_scores` to allow plotting scores in multiple columns, by `Luke Bloy`_

• In :func:`mne.stats.permutation_cluster_test` and :func:`mne.stats.permutation_cluster_1samp_test` the default parameter value out_type='mask' has changed to None, which in 0.21 means 'mask' but will change to mean 'indices' in the next version, by `Daniel McCloy`_

• The default window size set by filter_length when method='spectrum_fit' in :meth:`mne.io.Raw.notch_filter` will change from None (use whole file) to '10s' in 0.22, by `Eric Larson`_

• vmin and vmax parameters are deprecated in :meth:`mne.Epochs.plot_psd_topomap` and :func:`mne.viz.plot_epochs_psd_topomap`; use new vlim parameter instead, by `Daniel McCloy`_.

• The method stc_mixed.plot_surface for a :class:`mne.MixedSourceEstimate` has been deprecated in favor of :meth:`stc.surface().plot(...) <mne.MixedSourceEstimate.surface>` by `Eric Larson`_

• The method stc.normal for :class:`mne.VectorSourceEstimate` has been deprecated in favor of :meth:`stc.project('nn', src) <mne.VectorSourceEstimate.project>` by `Eric Larson`_

• Add use_dev_head_trans parameter to :func:`mne.preprocessing.annotate_movement` to allow choosing the device to head transform is used to define the fixed cHPI coordinates by `Luke Bloy`_

• The function mne.channels.read_dig_captrack will be deprecated in version 0.22 in favor of :func:`mne.channels.read_dig_captrak` to correct the spelling error: "captraCK" -> "captraK", by `Stefan Appelhoff`_

• The threshold argument in :meth:`mne.preprocessing.ICA.find_bads_ecg` defaults to None in version 0.21 but will change to 'auto' in 0.22 by `Yu-Han Luo`_

• The function mne.preprocessing.mark_flat has been deprecated in favor of mne.preprocessing.annotate_flat by `Eric Larson`_

• The default argument meg=True in :func:`mne.pick_types` will change to meg=False in version 0.22 by `Clemens Brunner`_

• Added :meth:`mne.io.Raw.get_montage`, which obtains the montage that an instance has, by `Adam Li`_

Authors

People who contributed to this release in alphabetical order (people with a + are first time contributors):

• Adam Li
• Adonay Nunes
• Alejandro Weinstein
• Alex Rockhill
• Alexandre Gramfort
• Anton Nikolas Waniek
• Britta Westner
• Christian O'Reilly
• Clemens Brunner
• Daniel McCloy
• Eric Larson
• Evgenii Kalenkovich
• Fede Raimondo
• Guillaume Favelier
• Hubert Banville
• Jeroen Van Der Donckt +
• Johann Benerradi +
• Kyle Mathewson +
• Lau Møller Andersen +
• Liberty Hamilton +
• Luke Bloy
• Lx37 +
• Mainak Jas
• Marijn van Vliet
• Martin Billinger
• Martin Schulz +
• Martin van Harmelen
• Mikolaj Magnuski
• Olaf Hauk
• Rahul Nadkarni +
• Richard Höchenberger
• Robert Luke
• Sara Sommariva
• Simeon Wong +
• Stefan Appelhoff
• Steven Bierer +
• Svea Marie Meyer +
• Teon Brooks
• Thomas Hartmann
• Yu-Han Luo
• chapochn
• mshader