v0.19.rst

Version 0.19 (2019-09-24)

Changelog

• Add :func:`mne.cuda.set_cuda_device` and config variable MNE_CUDA_DEVICE to select among multiple GPUs (by numeric device ID) by `Daniel McCloy`_.
• Add :func:`mne.channels.make_standard_montage` to create :class:`mne.channels.DigMontage` from templates by `Joan Massich`_ and `Alex Gramfort`_.
• Add :func:`mne.channels.compute_dev_head_t` to compute Device-to-Head transformation from a montage by `Joan Massich`_ and `Alex Gramfort`_.
• Add :func:`mne.channels.read_dig_fif` to read digitization coordinates from .fif files by `Joan Massich`_ and `Alex Gramfort`_.
• Add :func:`mne.channels.read_dig_egi` to read digitization coordinates from EGI .xml files by `Joan Massich`_ and `Alex Gramfort`_.
• Add :func:`mne.channels.read_dig_polhemus_isotrak` and :func:`mne.channels.read_polhemus_fastscan` to read Polhemus data by `Joan Massich`_
• Add mne.channels.read_dig_captrack to read BrainVision CapTrak (BVCT) digitization coordinate files by `Stefan Appelhoff`_ and `Joan Massich`_
• Add :func:`mne.channels.make_dig_montage` to create :class:`mne.channels.DigMontage` objects out of np.arrays by `Joan Massich`_
• Add :func:`mne.channels.read_custom_montage` to read various EEG electrode locations files by `Joan Massich`_ and `Alex Gramfort`_.
• Add support for making epochs with duplicated events, by allowing three policies: "error" (default), "drop", or "merge" in :class:`mne.Epochs` by `Stefan Appelhoff`_
• Allow :meth:`mne.Annotations.crop` to support negative tmin and tmax by `Joan Massich`_
• Unknown events code in GDF are now visible in the event_id by `Théodore Papadopoulo`_
• Now :func:`mne.io.read_raw_ctf` populates raw.annotations with the markers in MarkerFile.mrk if any by `Joan Massich`_
• Add options for controlling the use of the -T1 flag and the location of the brainmask output in :ref:`mne watershed_bem` by `Eric Larson`_
• Add support to :func:`mne.read_annotations` to read CTF marker files by `Joan Massich`_
• Do not convert effective number of averages (nave attribute of :class:`mne.Evoked`) to integer except when saving to FIFF file by `Daniel McCloy`_.
• Add automatic fiducial position estimation in :ref:`mne coreg` using MNI Talairach fiducial locations in :func:`mne.coreg.get_mni_fiducials` by `Jon Houck`_ and `Eric Larson`_
• Add support for :ref:`mne coreg` scaling surrogate subjects without surface reconstructions, such as those created for volumetric analyses only (e.g., with recon-all -autorecon1) by `Eric Larson`_
• Add reader for Curry data in :func:`mne.io.read_raw_curry` by `Dirk Gütlin`_
• Butterfly channel plots now possible for :meth:`mne.Epochs.plot_psd` with average=False. Infrastructure for this function now shared with analogous Raw function, found in mne.viz.utils by `Jevri Hanna`_
• Add option not to orthogonalize power envelopes with orthogonalize=False in mne.connectivity.envelope_correlation by `Denis Engemann`_
• Accept filenames of raw .fif files that end in _meg.fif to enable complicance with the Brain Imaging Data Structure by `Stefan Appelhoff`_
• Add function to check the type of a FIF file using :func:`mne.what` and :ref:`mne what` by `Eric Larson`_
• Add support for specifying the initial time and/or position and providing a :class:`mne.SourceMorph` instead of :class:`mne.SourceSpaces` in :func:`mne.viz.plot_volume_source_estimates` by `Eric Larson`_
• Speed up morph map generation in :func:`mne.read_morph_map` by ~5-10x by using :func:`numba.jit` by `Eric Larson`_
• Speed up :func:`mne.setup_volume_source_space`, especially when volume_label is not None by `Eric Larson`_
• Speed up :ref:`mne coreg` interactive and automated (ICP) alignment by using nearest-neighbor calculations in the MRI coordinate frame, by `Eric Larson`_
• Add :func:`mne.dig_mri_distances` to compute the distances between digitized head points and the MRI head surface by `Alex Gramfort`_ and `Eric Larson`_
• Add scale bars for data channels in :func:`mne.io.Raw.plot` by `Eric Larson`_
• Add :func:`mne.viz.plot_brain_colorbar` to plot a colorbar appropriately matched to a :func:`mne.viz.plot_source_estimates` plot by `Eric Larson`_
• Add support for showing head surface (to visualize digitization fit) while showing a single-layer BEM to :func:`mne.viz.plot_alignment` by `Eric Larson`_
• Add option include_tmax=True to cropping methods :meth:`mne.io.Raw.crop`, :meth:`mne.Epochs.crop`, :meth:`mne.Evoked.crop`, :meth:`mne.SourceEstimate.crop`, :meth:`mne.Dipole.crop`, and :meth:`mne.time_frequency.AverageTFR.crop` by `Eric Larson`_
• Change the behavior of :meth:`mne.io.Raw.plot` for scalings='auto' and remove_dc=True to compute the scalings on the data with DC removed by `Clemens Brunner`_
• Allow creating annotations within existing annotations in :func:`mne.io.Raw.plot` by default (the old snapping behavior can be toggled by pressing 'p') by `Clemens Brunner`_
• Add plotting of rank estimates in :func:`mne.viz.plot_cov` by `Eric Larson`_
• Add a new mne.viz.plot_sensors_connectivity function to visualize the sensor connectivity in 3D by `Guillaume Favelier`_ and `Alex Gramfort`_
• Add support for info['utc_offset'], info['device_info'], and info['helium_info'] components of :class:`mne.Info` by `Eric Larson`_
• Add control over dipole colors in :func:`mne.viz.plot_dipole_locations` when using orthoview mode by `Eric Larson`_
• Use second-order-sections filtering in :meth:`mne.io.Raw.plot` and :ref:`mne browse_raw` by `Eric Larson`_
• Add re-referencing functionality for ecog and seeg channel types in :func:`mne.set_eeg_reference` by `Keith Doelling`_
• Add support for median averaging and for returning unaggregated segments in mne.time_frequency.psd_welch by `Richard Höchenberger`_
• :func:`io.read_raw_kit`: add support for NYU New York 2019 system update, by `Christian Brodbeck`_

Bug

• Fix setting montage eeg ref position for captrak by `Joan Massich`_
• Fix saving raw read from BDF file using tmin and tmax using preload=False by `Alex Gramfort`_
• Fix :func:`mne.grand_average` to use equal sum-to-one weights (like it used to, before changes to underlying :func:`mne.combine_evoked`) by `Daniel McCloy`_
• Fix :meth:`mne.io.Raw.filter` to deal with instances with no data channels properly by `Eric Larson`_
• Fix one-sample baseline issue in :class:`mne.BaseEpochs` when using tmin=0 by `Milan Rybář`_
• Fix bug in :func:`mne.viz.plot_volume_source_estimates` where 'glass_brain' MRIs were not transformed to MNI space, by `Eric Larson`_
• Fix bug in :func:`mne.viz.plot_volume_source_estimates` where MRIs with voxels not in RAS orientation could not be browsed properly, by `Eric Larson`_
• Fix bug in :meth:`mne.SourceMorph.apply` where output STCs had stc.vertices defined improperly, by `Eric Larson`_
• Fix bug in :meth:`mne.SourceMorph.apply` where the default was errantly mri_space=False instead of mri_space=None (as documented), by `Eric Larson`_
• Fix mne.VolVectorSourceEstimate.normal and :func:`mne.minimum_norm.apply_inverse` to only allow normal extraction/orientation for surface and discrete source spaces by `Eric Larson`_
• Fix :meth:`mne.io.Raw.set_annotations` for meas_date previous to 1970 by `Joan Massich`_
• Fix horizontal spacing issues in :meth:`mne.io.Raw.plot_psd` by `Jevri Hanna`_
• Fix reading of dates in BrainVision files if no "New Segment" marker is specified, no date is given, or data is missing, by `Stefan Appelhoff`_
• Fix bug with reading one-channel GDF files by `Abram Hindle`_
• Fix bug with y-axis labeling in :meth:`mne.io.Raw.plot_psd` by `Eric Larson`_
• Fix side-effect where :func:`mne.viz.plot_ica_sources` and :meth:`mne.preprocessing.ICA.plot_sources` changed the ICA.exclude attribute even when users didn't interact with the plot by `Daniel McCloy`_.
• Fix scaling of sources in :meth:`ica.plot_sources(epochs) <mne.preprocessing.ICA.plot_sources>` by `Eric Larson`_
• Fix wrong assumptions about units in BrainVision montages and add test asserting units in "mm" or "auto", by `Stefan Appelhoff`_
• Fix scaling issue with signals in mV in EDF files read with :func:`mne.io.read_raw_edf` by `Alex Gramfort`_
• Fix :func:`mne.extract_label_time_course` behavior when using STCs generated with apply_inverse(..., label=label) or stc.in_label by `Eric Larson`_
• Fix bug in :func:`mne.io.read_raw_brainvision` so that recording date timestamps are also recognized if channel reference data is negative, by `Stefan Appelhoff`_
• Fix order of info['dig'] that was alphabetical based on channel names and not following the channel order when using :meth:`mne.io.Raw.set_montage` and a mne.channels.Montage object by `Joan Massich`_ and `Alex Gramfort`_.
• Fix reading CNT files larger than 2Gb by `Joan Massich`_
• Fix reading of 4D/BTi data with different channel names and onsets in :func:`mne.io.read_raw_bti` by `Joshua Bear`_ and `Eberhard Eich`_
• Fix formula for effective number of averages in :func:`mne.combine_evoked` when weights='equal' by `Daniel McCloy`_.
• Fix bug in :func:`mne.simulation.simulate_stc` to avoid empty stc if label vertices and source space do not intersect, by `Kostiantyn Maksymenko`_
• Fix event_id='auto' in :func:`mne.events_from_annotations` to recover Brainvision markers after saving it in .fif by `Joan Massich`_
• Fix :func:`mne.read_epochs_eeglab` when epochs are stored as float. By `Thomas Radman`_
• Fix :func:`mne.Evoked.resample` and :func:`mne.Epochs.resample` not setting inst.info['lowpass'] properly by `Eric Larson`_
• Fix checks when constructing volumetric and surface source spaces with :func:`mne.setup_volume_source_space` and :func:`mne.setup_source_space`, respectively, by `Eric Larson`_
• Fix bug in handling of :class:`mne.Evoked` types that were not produced by MNE-Python (e.g., alternating average) by `Eric Larson`_
• Fix bug in :func:`mne.read_source_estimate` where vector volumetric source estimates could not be read by `Eric Larson`_
• Fix bug in :func:`mne.inverse_sparse.mixed_norm` and :func:`mne.inverse_sparse.tf_mixed_norm` where weights was supplied but weights_min was not, by `Eric Larson`_
• Fix bug in :func:`mne.set_eeg_reference` where non-EEG channels could be re-referenced by default if there were no EEG channels present, by `Eric Larson`_
• Fix bug in :func:`mne.io.Raw.plot` when using HiDPI displays and the MacOSX backend of matplotlib by `Eric Larson`_
• Fix bug in :func:`mne.viz.plot_compare_evokeds` when using Neuromag 122 system by `Eric Larson`_
• Fix bug in :func:`mne.Epochs.plot_psd` when some channels had zero/infinite psd values causing erroneous error messages by `Luke Bloy`_
• Fix :func:`mne.Evoked.decimate` not setting inst.first and inst.last properly by `Marijn van Vliet`_
• Fix :func:`mne.io.read_raw_brainvision` not handling Event markers created by PyCorder correctly by `Richard Höchenberger`_
• Fix support for string-like objects (such as :class:`python:pathlib.Path`) by `Eric Larson`_
• Fix :class:`mne.Report` silently suppressing exceptions when used as a context manager by `Marijn van Vliet`_

API

• Deprecate mne.channels.Montage class, mne.channels.read_montage and mne.channels.read_dig_montage function by `Joan Massich`_.
• Deprecate passing Montage, str as montage parameter in :meth:`mne.io.Raw.set_montage` by `Joan Massich`_.
• Deprecate set_dig parameter in :meth:`mne.io.Raw.set_montage` and update_ch_names in mne.io.RawEEGLAB.set_montage when using :class:`mne.channels.DigMontage` as by `Joan Massich`_.
• Now :meth:`mne.io.Raw.set_montage` raises an error when :class:`mne.channels.DigMontage` contains only a subset of the channels in raw.info. It also adds raise_if_subset parameter to ensure backward compatibility (defaults to False in 0.19, to True in 0.20, and will be removed in 0.21) by `Joan Massich`_.
• Minimum dependency versions for the following libraries have been bumped up (by `Eric Larson`_):
  • NumPy: 1.12.1
  • SciPy: 0.18.1
  • matplotlib: 2.0.2
  • scikit-learn: 0.18.2
  • pandas 0.19.2
• New boolean parameter show_scrollbars for :meth:`mne.io.Raw.plot`, :meth:`mne.Epochs.plot`, and :meth:`mne.preprocessing.ICA.plot_sources` (and associated functions) that allows hiding the scrollbars and buttons for a "zen mode" data browsing experience. When the plot window has focus, zen mode can be toggled by pressing z, by `Daniel McCloy`_.
• Deprecate mne.evoked.grand_average in favor of :func:`mne.grand_average` (which works on both :class:`~mne.Evoked` and :class:`~mne.time_frequency.AverageTFR`) by `Daniel McCloy`_
• Deprecate exclude parameter in :func:`mne.viz.plot_ica_sources` and :meth:`mne.preprocessing.ICA.plot_sources`, instead always use the exclude attribute of the ICA object by `Daniel McCloy`_.
• Deprecate montage parameter in favor of the set_montage method in all EEG data readers :func:`mne.io.read_raw_cnt`, :func:`mne.io.read_raw_egi`, :func:`mne.io.read_raw_edf`, :func:`mne.io.read_raw_gdf`, :func:`mne.io.read_raw_nicolet`, :func:`mne.io.read_raw_eeglab` and :func:`mne.read_epochs_eeglab` by `Alex Gramfort`_
• New parameter clear in :func:`mne.viz.plot_epochs_image` for clearing pre-existing axes before plotting into them by `Daniel McCloy`_
• :func:`mne.viz.plot_epochs_image` no longer supports group_by='type' — combining by channel type is now the default when picks is a channel type string; to get individual plots for each channel, pass picks as a list of channel names or indices by `Daniel McCloy`_
• New parameter combine in :func:`mne.viz.plot_compare_evokeds` for specifying method to combine information across channels by `Daniel McCloy`_
• FIFF constants related to SmartShield (*_SMSH_* and *_SMARTSHIELD) have been renamed to IAS for consistency with MEGIN, by `Eric Larson`_
• The gfp parameter of :func:`mne.viz.plot_compare_evokeds` is deprecated; use combine='gfp' instead by `Daniel McCloy`_
• The truncate_yaxis='max_ticks' parameter of :func:`mne.viz.plot_compare_evokeds` is deprecated; use truncate_yaxis='auto' instead by `Daniel McCloy`_
• The truncate_xaxis and truncate_yaxis parameters of :func:`mne.viz.plot_compare_evokeds` now perform one-sided truncation unless both are True by `Daniel McCloy`_
• The show_legend parameter of :func:`mne.viz.plot_compare_evokeds` is renamed to legend by `Daniel McCloy`_
• :func:`mne.viz.plot_compare_evokeds` always returns a list of figures even when a single figure is generated by `Daniel McCloy`_
• Deprecate average=True and spatial_colors=False for :func:`mne.Epochs.plot_psd` by `Jevri Hanna`_
• :func:`mne.io.read_raw_brainvision` no longer raises an error when there are inconsistencies between info['chs'] and montage but warns instead by `Joan Massich`_
• Add update_ch_names parameter to mne.io.RawEEGLAB.set_montage to allow updating the channel names based on the montage by `Joan Massich`_
• Reading annotations contained in GDF files with :func:`mne.io.read_raw_gdf` now returns numeric event codes as descriptions (instead of textual descriptions) due to restrictive licensing of the GDF event code table from BioSig by `Clemens Brunner`_
• channels.find_ch_connectivity now returns pre-built neighbor maps for KIT systems when available, by `Christian Brodbeck`_