v1.1.rst

Version 1.1.0 (2022-08-03)

Enhancements

• Added new built-in montage R-Net 128 Ch (Brain Products) (:gh:`10974` by :newcontrib:`Ilias Machairas`)
• :class:`~mne.channels.DigMontage` objects can now be checked for equality via == (:gh:`10942` by :newcontrib:`Tziona NessAiver`)
• Add a note to clarify the inclusion of average referencing gain matrix during whitening (:gh:`10922` by :newcontrib:`Mingjian He`)
• Add time axis scale bar for :meth:`mne.Epochs.plot` using matplotlib backend (:gh:`10736` by :newcontrib:`Jordan Drew`)
• Add :func:`mne.bem.distance_to_bem` to find depth of source positions (:gh:`10632` by :newcontrib:`Matt Courtemanche`)
• Add support for ahdr files in :func:`mne.io.read_raw_brainvision` (:gh:`10515` by :newcontrib:`Alessandro Tonin`)
• Add support for reading data from Gowerlabs devices to :func:`mne.io.read_raw_snirf` (:gh:`10555` by :newcontrib:`Samuel Powell` and `Robert Luke`_)
• Add built-in sensor layout files for Geodesic Head Web 130 and 280 devices (:gh:`10627` by `Evan Hathaway`_)
• Add mne-icalabel to :func:`mne.sys_info` (:gh:`10615` by `Adam Li`_)
• Add support for overview_mode in :meth:`raw.plot() <mne.io.Raw.plot>` and related functions/methods (:gh:`10501` by `Eric Larson`_)
• Add :meth:`mne.io.Raw.crop_by_annotations` method to get chunks of Raw data based on :class:`mne.Annotations`. (:gh:`10460` by `Alex Gramfort`_)
• The pick_channels method gained a verbose parameter, allowing e.g. to suppress messages about removed projectors (:gh:`10544` by `Richard Höchenberger`_)
• Add :func:`mne.viz.plot_projs_joint` for joint plotting of projectors and Evoked (:gh:`10720` by `Eric Larson`_)
• The :func:`mne.make_forward_dipole` function can now take a list of dipoles to make a multi-dipole forward models (:gh:`10464` by `Marijn van Vliet`_)
• Add mode='outlines' support to :meth:`mne.Dipole.plot_locations` and :func:`mne.viz.plot_dipole_locations` (:gh:`10699` by `Eric Larson`_)
• Add :meth:`mne.preprocessing.ICA.find_bads_muscle` to find muscle-related ICA components with an example, :ref:`ex-muscle-ica` (:gh:`10534` by `Alex Rockhill`_)
• Add example of Xfit-style ECD modeling using multiple dipoles (:gh:`10464` by `Marijn van Vliet`_)
• Add head_source argument to :func:`mne.make_field_map` to allow selecting which head source to use (:gh:`10568` by `Eric Larson`_)
• Add support for n_jobs=None to support joblib:joblib.parallel_backend for more precise control over parallelization (:gh:`10567` by `Eric Larson`_)
• It is now possible to compute inverse solutions with restricted source orientations using discrete forward models (:gh:`10464` by `Marijn van Vliet`_)
• The new function :func:`mne.preprocessing.maxwell_filter_prepare_emptyroom` simplifies the preconditioning of an empty-room recording for our Maxwell filtering operations (:gh:`10533` by `Richard Höchenberger`_ and `Eric Larson`_)
• Add keyboard shortcuts to toggle :meth:`mne.preprocessing.ICA.plot_properties` topomap channel types ('t') and power spectral density log-scale ('l') (:gh:`10557` by `Alex Rockhill`_)
• Add --mri, and --threshold options to :ref:`mne make_scalp_surfaces` to improve head surface mesh extraction (:gh:`10591` by `Eric Larson`_)
• Add :func:`mne.preprocessing.compute_bridged_electrodes` to detect EEG electrodes with shared spatial sources due to a conductive medium connecting two or more electrodes, add :ref:`ex-eeg-bridging` for an example and :func:`mne.viz.plot_bridged_electrodes` to help visualize (:gh:`10571` by `Alex Rockhill`_)
• Add 'nearest' as an option for the image_interp argument in :func:`mne.viz.plot_topomap` to plot a topomap without interpolation using a Voronoi parcelation (:gh:`10571` by `Alex Rockhill`_)
• Add :func:`mne.preprocessing.interpolate_bridged_electrodes` to use the spatially smeared signal to get a better interpolation rather than dropping those channels (:gh:`10587` by `Alex Rockhill`_)
• Add support for hemoglobin type fNIRS data to temporal derivative distribution repair (TDDR) :func:`mne.preprocessing.nirs.temporal_derivative_distribution_repair` (:gh:`10125` by `Johann Benerradi`_)
• :func:`mne.viz.plot_evoked_topomap` and :meth:`mne.Evoked.plot_topomap` now display the time range the map was averaged over if average was passed (:gh:`10606` by `Richard Höchenberger`_)
• :func:`mne.viz.plot_evoked_topomap` and :meth:`mne.Evoked.plot_topomap` can now average the topographic maps across different time periods for each time point. To do this, pass a list of periods via the average parameter (:gh:`10610` by `Richard Höchenberger`_)
• :func:`mne.viz.plot_evoked` and :meth:`mne.Evoked.plot` gained a new parameter, highlight, to visually highlight time periods of interest (:gh:`10614` by `Richard Höchenberger`_)
• Added fNIRS support to :func:`mne.Info.get_montage` (:gh:`10611` by `Robert Luke`_)
• Add :func:`mne.viz.plot_ch_adjacency` to visualize and manually edit the channel adjacency matrix (:gh:`10633` by `Mikołaj Magnuski`_)
• Add :meth:`mne.viz.Brain.get_view` to get the current camera parameters such that they can be passed to :meth:`mne.viz.Brain.show_view` (:gh:`10661` by `Alex Rockhill`_)
• Added support for Aurora version 2021.9.0.6 to :func:`mne.io.read_raw_nirx` (:gh:`10668` by `Robert Luke`_)
• Added BrainVision format (.vhdr, .vmrk, .eeg) to :func:`mne.export.export_raw` (:gh:`10681` by `Stefan Appelhoff`_)
• Added export method to :class:`mne.Evoked` (:gh:`10681` by `Stefan Appelhoff`_)
• Add timeformat YYYY/MM/DD to mne.io.ctf.info._convert_time (:gh:`10674` by `Simon Kern`_)
• :meth:`mne.Report.add_figure` and :meth:`mne.Report.add_image` gained a new parameter, section, allowing to put multiple figures or images into the same "content block". Previously, the only way to group figures and images was by means of a slider, which sometimes made content hard to discover. The slider remains available as an alternative (:gh:`10694` by `Richard Höchenberger`_)
• All functions and methods that plot topographic maps for EEG (2D projections of the EEG sensor locations) now accept the parameter value sphere='eeglab' to lay out the sensors with respect to the head circle in a similar way to how EEGLAB does, i.e., T7/T8 and Fpz/Oz are placed directly on the circle for template montages (:gh:`10572` by `Richard Höchenberger`_)
• :func:`mne.channels.get_builtin_montages` gained a new parameter, descriptions, which allows to retrieve the descriptions of the montages in addition to their names (:gh:`10373` by `Richard Höchenberger`_)
• Add include option to :meth:`mne.io.read_raw_edf`, :meth:`mne.io.read_raw_bdf` and :meth:`mne.io.read_raw_gdf`. (:gh:`10734` by `Michiru Kaneda`_)
• :func:`mne.gui.coregistration` gained a new parameter, fullscreen, to start the GUI in fullscreen mode (:gh:`10284` by `Richard Höchenberger`_)
• The built-in FieldTrip channel adjacency matrices, which can be read via :func:`~mne.channels.read_ch_adjacency`, have been synchronized with FieldTrip again. This means that numerous new adjacencies have been added, most notably those for standard 10-05 and 10-20 montages (:gh:`10749` by `Richard Höchenberger`_)
• :meth:`mne.Evoked.plot_field` gained a new parameter, interaction, to control the rotation axes when interacting with the head (:gh:`10788` by `Richard Höchenberger`_)
• Add :func:`mne.read_evoked_besa` for reading evokeds from BESA .avr and .mul files. (:gh:`10892` by `Marijn van Vliet`_)
• Add :meth:`mne.time_frequency.EpochsTFR.decimate` to reduce size of time-frequency epochs objects (:gh:`10940` by `Alex Rockhill`_)
• Add an alias that maps EGI reference channel names (VREF or Vertex Reference) to the electrode name in the standard EGI montages (Cz). Now setting standard EGI montages with :meth:`~mne.io.Raw.set_montage` with match_alias=True will avoid raising an error (:gh:`10823` by `Scott Huberty`_)
• Add provenance in :func:`mne.time_frequency.EpochsTFR.apply_baseline` (:gh:`10979` by `Alex Rockhill`_)

Bugs

• Fix bug in mne.surface._project_onto_surface for the condition method != 'accurate' and return_nn (:gh:`10930` by `Christian O'Reilly`_)
• Fix bug in :func:`mne.export.export_raw` to ignore None value in filenames attribute of :class:`mne.io.RawArray` (:gh:`10927` by :newcontrib:`Reza Nasri`)
• Fix bug in :func:`mne.io.read_raw_edf` to allow reading in all Hypnodyne ZMax EDFs to be read in without issues (:gh:`10754` by :newcontrib:`Frederik Weber`)
• Fix bug in :func:`mne.Epochs.drop_bad` where data was loaded although no rejection had to be performed (:gh:`10718` by :newcontrib:`Lukas Gemein`)
• Pick also bad channels when selecting T1T2 magnetometers in :func:`mne.preprocessing.maxwell_filter` (:gh:`10639` by :newcontrib:`Matti Toivonen`)
• Make color parameter check in in :func:`mne.viz.plot_evoked_topo` consistent (:gh:`10217` by :newcontrib:`T. Wang` and `Stefan Appelhoff`_)
• Fix bug in :func:`mne.io.read_raw_brainvision` when BrainVision data are acquired with the Brain Products "V-Amp" amplifier and disabled lowpass filter is marked with value 0 (:gh:`10517` by :newcontrib:`Alessandro Tonin`)
• Fix bug in :func:`mne.pick_types` and related methods where csd=True was not passed handled properly (:gh:`10470` by :newcontrib:`Matthias Dold`)
• Fix bug where plots produced using the 'qt' / mne_qt_browser backend could not be added using :meth:`mne.Report.add_figure` (:gh:`10485` by `Eric Larson`_)
• Fix bug where theme was not handled properly in :meth:`mne.io.Raw.plot` (:gh:`10487`, :gh:`10500` by `Mathieu Scheltienne`_ and `Eric Larson`_)
• Fix bug in :meth:`raw.crop(start, stop) <mne.io.Raw.crop>` that would cause annotations to be erroneously shifted when start != 0 and no measurement date was set. (:gh:`10491` by `Eric Larson`_)
• Fix bug in :func:`mne.io.read_raw_bti` where unknown electrode locations were not handled properly (:gh:`10662` by `Eric Larson`_)
• Fix bug in :func:`mne.io.read_raw_ctf` on Windows where large files could not be read (:gh:`10866` by `Eric Larson`_)
• Fix bug in :func:`mne.io.read_raw_ctf` where invalid measurement dates were not handled properly (:gh:`10957` by `Jean-Rémi King`_ and `Eric Larson`_)
• Rendering issues with recent MESA releases can be avoided by setting the new environment variable MNE_3D_OPTION_MULTI_SAMPLES=1 or using :func:`mne.viz.set_3d_options` (:gh:`10513` by `Eric Larson`_)
• Fix behavior for the pyvista 3D renderer's quiver3D function so that default arguments plot a glyph in arrow mode (:gh:`10493` by `Alex Rockhill`_)
• Retain epochs metadata when using :func:`mne.channels.combine_channels` (:gh:`10504` by `Clemens Brunner`_)
• Fix epochs indexing with metadata containing boolean type and missing values (:gh:`10705` by `Clemens Brunner`_ and `Alex Gramfort`_)
• Fix reading of fiducial locations in :func:`mne.io.read_raw_eeglab` (:gh:`10521` by `Alex Gramfort`_)
• Prevent creation of montage with invalid [x, y, z] coordinates with :func:`mne.channels.make_dig_montage` (:gh:`10547` by `Mathieu Scheltienne`_)
• Fix bug in coregistration GUI that prevented it from starting up if only a high-resolution head model was available (:gh:`10543` by `Richard Höchenberger`_)
• Fix bug with :class:`mne.Epochs.add_reference_channels` where attributes were not updated properly so subsequent ~mne.Epochs.pick_types calls were broken (:gh:`10912` by `Eric Larson`_)
• Fix bug in the :class:`mne.viz.Brain` tool bar that prevented the buttons to call the corresponding feature (:gh:`10560` by `Guillaume Favelier`_)
• Fix issue with saving epochs once :func:`~mne.preprocessing.compute_current_source_density` has been used if a rejection threshold was used first (:gh:`10619` by `Alex Rockhill`_ and `Richard Höchenberger`_)
• Fix bug in :func:`mne.viz.plot_evoked_image` that would cause incorrect sub-titles when using group_by (:gh:`10618` by `Reza Shoorangiz`_)
• Reduce memory usage when loading an EDF file with preload=False (:gh:`10638` by `Clemens Brunner`_)
• Fix bug in :meth:`mne.io.Raw.get_channel_types` and related methods where unique=True would return a :class:`python:set` with arbitrary order rather than a :class:`python:list` that preserves the same order as inst.ch_names (:gh:`10720` by `Eric Larson`_)
• In :func:`mne.preprocessing.find_bad_channels_maxwell`, do not re-filter the data if a low-pass filter with the requested frequency has already been applied (:gh:`10664` by `Richard Höchenberger`_)
• Fix a problem in :meth:`mne.Evoked.get_peak`, where under certain circumstances the mode parameters 'pos' and 'neg' were not honored when tmin and/or tmax were passed as well (:gh:`10686` by `Richard Höchenberger`_)
• :func:`mne.read_evokeds`, :func:`mne.channels.read_custom_montage`, :func:`mne.channels.read_dig_hpts`, :func:`mne.channels.read_dig_polhemus_isotrak`, and :func:`mne.channels.read_polhemus_fastscan` now correctly expand ~ in the provided path to the user's home directory (:gh:`10685`, :gh:`10688` by `Richard Höchenberger`_)
• Fix bug in :func:`mne.io.read_raw_eeglab` and :func:`mne.read_epochs_eeglab`, where the presence of channels without position in the .set file caused positions incorrectly assigned to all further channels (:gh:`8754` by `Mikołaj Magnuski`_)
• Combining channels of :class:`mne.Epochs` or :class:`mne.Evoked` objects now properly retains baseline information (:gh:`10703` by `Clemens Brunner`_)
• In :class:`mne.Report`, some figures would have an undesired border added to the edges; this has now been resolved (:gh:`10730` by `Richard Höchenberger`_)
• Fix selection of EEG channels and selected sphere when plotting bridged electrodes with :func:`mne.viz.plot_bridged_electrodes` (:gh:`10753` by `Mathieu Scheltienne`_)
• Fix broken links in :ref:`tut-fix-meshes` (:gh:`10765` by `Alex Rockhill`_)
• The built-in FieldTrip channel adjacency matrix for easycapM1 had a bug, where the channel PO8 was incorrectly labeled as PO6 This has been resolved by updating the adjacency matrix to the latest version provided by FieldTrip (:gh:`10749` by `Richard Höchenberger`_)
• Add a YouTube video tutorial for editing Freesurfer surfaces in Blender to :ref:`tut-fix-meshes` (:gh:`10778` by `Alex Rockhill`_)
• The default interaction style of :meth:`mne.Evoked.plot_field` has been changed such that if behaves like :func:`~mne.viz.plot_alignment` when trying to rotate the head (:gh:`10788` by `Richard Höchenberger`_)
• Add a video on how to operate the intracranial electrode contact location GUI in :ref:`tut-ieeg-localize` (:gh:`10800` by `Alex Rockhill`_)
• Add a video on how to operate the coregistration GUI in :ref:`tut-source-alignment` (:gh:`10802` by `Alex Rockhill`_)
• Add show and block arguments to :func:`mne.gui.coregistration` and mne.gui.locate_ieeg to pop up the GUIs and halt execution of subsequent code respectively (:gh:`10802` by `Alex Rockhill`_)
• Correctly report the number of available projections when printing measurement info in a Jupyter notebook (:gh:`10471` by `Clemens Brunner`_)
• Fix value set in raw.orig_format for readers of BrainVision (ASCII format), EGI and Artemis123 files (:gh:`10851` by `Mathieu Scheltienne`_)
• When reading EGI MFF files, channel names are no longer ignored and reference channel information is properly incorporated (:gh:`10898` by `Scott Huberty`_ and `Daniel McCloy`_)
• Fix bug in :func:`mne.time_frequency.psd_array_welch` and related functions/methods where the bias was not accounted for when average='median' (:gh:`10990` by `Eric Larson`_)
• Fix bug in :class:`mne.decoding.TemporalFilter` where filter parameters were not handled properly (:gh:`10968` by `Eric Larson`_)
• Fix documentation bug in ica.plot_sources to specify that picks keyword argument is for picking ICA components to plot (:gh:`10936` by `Adam Li`_)
• Annotations contained in EDF files are correctly read as UTF-8 according to the EDF specification (:gh:`10963` by `Clemens Brunner`_)
• Fix bug where complex-valued topoplots caused an error, convert to amplitude instead (:gh:`10978` by `Alex Rockhill`_)

API and behavior changes

• When creating BEM surfaces via :func:`mne.bem.make_watershed_bem` and :func:`mne.bem.make_flash_bem`, the copy parameter now defaults to True. This means that instead of creating symbolic links inside the FreeSurfer subject's bem folder, we now create "actual" files. This should avoid troubles when sharing files across different operating systems and file systems (:gh:`10531` by `Richard Höchenberger`_)
• The ordering of channels returned by :func:`mne.io.read_raw_nirx` is now ordered by channel name, rather than the order provided by the manufacturer. This enables consistent ordering of channels across different file types (:gh:`10555` by `Robert Luke`_)
• For :func:`mne.viz.plot_topomap`, :func:`mne.viz.plot_evoked_topomap`, :func:`mne.viz.plot_arrowmap`, :func:`mne.viz.plot_ica_components`, :meth:`mne.Covariance.plot_topomap`, :meth:`mne.Evoked.plot_topomap`, :meth:`mne.Evoked.animate_topomap`, :meth:`mne.decoding.CSP.plot_patterns`, :meth:`mne.Projection.plot_topomap` and :meth:`mne.preprocessing.ICA.plot_components` the topomap image interpolation was previously a cubic interpolation but now can be 'linear' and 'nearest' as well. Unless image_interp='nearest' is passed mne uses a subsequent matplotlib bilinear interpolation to make the interpolated image smoother. Previously, 'image_interp' controlled this second interpolation step and, for the first interpolation, the only option was cubic. To simplify, image_interp is now responsible for the main interpolation and the subsequent matplotlib image interpolation is bilinear but can be changed afterward using im.set_interpolation (:gh:`10617` by `Alex Rockhill`_)
• The FLASH BEM surface generation via :func:`mne.bem.make_flash_bem` or the :ref:`mne flash_bem` command has now been clarified in terms of expected inputs. In :func:`mne.bem.convert_flash_mris` the convert parameter is now deprecated and the flash5 and flash30 now accept list of file names or nibabel images. One breaking change is that now the flash files are looked for as mef05_*.mgz and mef30_*.mgz in mri/flash folder (:gh:`10715` by `Alex Gramfort`_)
• :func:`~mne.viz.plot_compare_evokeds` gets a new parameter time_unit which can be "s" or "ms" (:gh:`10950` by `Daniel McCloy`_)
• The to_data_frame methods for :meth:`Raw <mne.io.Raw.to_data_frame>`, :meth:`Epochs <mne.Epochs.to_data_frame>`, :meth:`Evoked <mne.Evoked.to_data_frame>`, :meth:`SourceEstimate <mne.SourceEstimate.to_data_frame>`, :meth:`EpochsTFR <mne.time_frequency.EpochsTFR.to_data_frame>`, and :meth:`AverageTFR <mne.time_frequency.AverageTFR.to_data_frame>` all now have default time_format=None (keep time in seconds) instead of time_format='ms' (convert time to milliseconds) (:gh:`10925` by `Daniel McCloy`_)
• :func:`mne.Evoked.decimate` now aligns to the sample at time=0 (so that the exact sample when the event occurred is preserved) to be consistent with :func:`mne.Epochs.decimate` (:gh:`10945` by `Alex Rockhill`_)

Authors

• Adam Li
• Adeline Fecker+
• Alessandro Tonin+
• Alex Ciok+
• Alex Rockhill
• Alexandre Gramfort
• Archit Singhal+
• Ashley Drew+
• Ben Beasley+
• Carina Forster+
• Christian O'Reilly
• Clemens Brunner
• Cora Kim
• Daniel McCloy
• Dominik Welke
• Dominique Makowski
• Eric Larson
• Evan Hathaway
• Frederik D. Weber+
• Guillaume Favelier
• Hamid Maymandi+
• Ilias Machairas+
• Jean-Rémi King
• Johann Benerradi
• Jon Houck
• Jona Sassenhagen
• Jordan Drew+
• Lukas Gemein+
• Marijn van Vliet
• Martin Schulz
• Mathieu Scheltienne
• Matt Courtemanche+
• Matthias Dold+
• Matti Toivonen+
• Michiru Kaneda+
• Mikołaj Magnuski
• Mingjian He+
• Naveen Srinivasan+
• Phillip Alday
• Reza Nasri+
• Reza Shoorangiz
• Richard Höchenberger
• Rob Luke
• Scott Huberty+
• Simon Kern
• Sondre Foslien+
• Stefan Appelhoff
• 20. Wang+
• Tziona NessAiver+