v0.15.rst

Version 0.15 (2017-10-20)

Changelog

• :meth:`mne.channels.Layout.plot` and :func:`mne.viz.plot_layout` now allows plotting a subset of channels with picks argument by `Jaakko Leppakangas`_
• Add .bvef extension (BrainVision Electrodes File) to mne.channels.read_montage by `Jean-Baptiste Schiratti`_
• Add :func:`mne.decoding.cross_val_multiscore` to allow scoring of multiple tasks, typically used with :class:`mne.decoding.SlidingEstimator`, by `Jean-Rémi King`_
• Add :class:`mne.decoding.ReceptiveField` module for modeling electrode response to input features by `Chris Holdgraf`_
• Add :class:`mne.decoding.TimeDelayingRidge` class, used by default by :class:`mne.decoding.ReceptiveField`, to speed up auto- and cross-correlation computations and enable Laplacian regularization by `Ross Maddox`_ and `Eric Larson`_
• Add new :mod:`mne.datasets.mtrf <mne.datasets.mtrf.data_path>` dataset by `Chris Holdgraf`_
• Add example of time-frequency decoding with CSP by `Laura Gwilliams`_
• Add :class:`mne.decoding.SPoC` to fit and apply spatial filters based on continuous target variables, by `Jean-Rémi King`_ and `Alexandre Barachant`_
• Add Fieldtrip's electromyogram dataset, by `Alexandre Barachant`_
• Add reject_by_annotation option to :func:`mne.preprocessing.find_eog_events` (which is also utilised by :func:`mne.preprocessing.create_eog_epochs`) to omit data that is annotated as bad by `Jaakko Leppakangas`_
• Add example for fast screening of event-related dynamics in frequency bands by `Denis Engemann`_
• Add :meth:`mne.time_frequency.EpochsTFR.save` by `Jaakko Leppakangas`_
• Add butterfly mode (toggled with 'b' key) to :meth:`mne.io.Raw.plot` by `Jaakko Leppakangas`_
• Add axes parameter to plot_topo functions by `Jaakko Leppakangas`_
• Add options to change time windowing in :func:`mne.chpi.filter_chpi` by `Eric Larson`_
• mne.channels.Montage.plot, :meth:`mne.channels.DigMontage.plot`, and :func:`mne.viz.plot_montage` now allow plotting channel locations as a topomap by `Clemens Brunner`_
• Add background_color parameter to :meth:`mne.Evoked.plot_topo` and :func:`mne.viz.plot_evoked_topo` and improve axes rendering as done in :func:`mne.viz.plot_compare_evokeds` by `Alex Gramfort`_
• Add support for GDF files in :func:`mne.io.read_raw_edf` by `Nicolas Barascud`_
• Add mne.io.find_edf_events for getting the events as they are in the EDF/GDF header by `Jaakko Leppakangas`_
• Speed up :meth:`mne.io.Raw.plot` and :meth:`mne.Epochs.plot` using (automatic) decimation based on low-passing with decim='auto' parameter by `Eric Larson`_ and `Jaakko Leppakangas`_
• Add mne.inverse_sparse.mxne_optim.dgap_l21l1 for computing the duality gap for TF-MxNE as the new stopping criterion by `Daniel Strohmeier`_
• Add option to return a list of :class:`Dipole` objects in sparse source imaging methods by `Daniel Strohmeier`_
• Add :func:`mne.inverse_sparse.make_stc_from_dipoles` to generate stc objects from lists of dipoles by `Daniel Strohmeier`_
• Add mne.channels.find_ch_connectivity that tries to infer the correct connectivity template using channel info. If no template is found, it computes the connectivity matrix using :class:`Delaunay <scipy.spatial.Delaunay>` triangulation of the 2d projected channel positions by `Jaakko Leppakangas`_
• Add IO support for EGI MFF format by `Jaakko Leppakangas`_ and `ramonapariciog`_
• Add option to use matplotlib backend when plotting with :func:`mne.viz.plot_source_estimates` by `Jaakko Leppakangas`_
• Add mne.channels.Montage.get_pos2d to get the 2D positions of channels in a montage by `Clemens Brunner`_
• Add MGH 60- and 70-channel standard montages to mne.channels.read_montage by `Eric Larson`_
• Add option for embedding SVG instead of PNG in HTML for :class:`mne.Report` by `Eric Larson`_
• Add confidence intervals, number of free parameters, and χ² to :func:`mne.fit_dipole` and :func:`mne.read_dipole` by `Eric Larson`_
• :attr:`mne.SourceEstimate.data` is now writable, writing to it will also update :attr:`mne.SourceEstimate.times` by `Marijn van Vliet`_
• :meth:`mne.io.Raw.plot` and :meth:`mne.Epochs.plot` now use anti-aliasing to draw signals by `Clemens Brunner`_
• Allow using saved DigMontage to import digitization to :func:`mne.gui.coregistration` by `Jaakko Leppakangas`_
• Add function :func:`mne.channels.get_builtin_montages` to list all built-in montages by `Clemens Brunner`_
• :class:`mne.decoding.SlidingEstimator` and :class:`mne.decoding.GeneralizingEstimator` now accept **fit_params at fitting by `Jean-Rémi King`_
• Add :class:`mne.VectorSourceEstimate` class which enables working with both source power and dipole orientations by `Marijn van Vliet`_
• Add option pick_ori='vector' to :func:`mne.minimum_norm.apply_inverse` to produce :class:`mne.VectorSourceEstimate` by `Marijn van Vliet`_
• Add support for :class:`numpy.random.RandomState` argument to seed in :mod:`statistical clustering functions <mne.stats>` and better documentation of exact 1-sample tests by `Eric Larson`_
• Extend :func:`mne.viz.plot_epochs_image`/:meth:`mne.Epochs.plot_image` with regards to grouping by or aggregating over channels. See the new example at examples/visualization/plot_roi_erpimage_by_rt.py by `Jona Sassenhagen`_
• Add bootstrapped confidence intervals to :func:`mne.viz.plot_compare_evokeds` by `Jona Sassenhagen`_ and `Denis Engemann`_
• Add example on how to plot ERDS maps (also known as ERSP) by `Clemens Brunner`_
• Add support for volume source spaces to spatial_src_connectivity and spatio_temporal_src_connectivity by `Alex Gramfort`_
• Plotting raw data (:func:`mne.viz.plot_raw` or :meth:`mne.io.Raw.plot`) with events now includes event numbers (if there are not more than 50 events on a page) by `Clemens Brunner`_
• Add filtering functions :meth:`mne.Epochs.filter` and :meth:`mne.Evoked.filter`, as well as pad argument to :meth:`mne.io.Raw.filter` by `Eric Larson`_
• Add high frequency somatosensory MEG dataset by `Jussi Nurminen`_
• Add reduced set of labels for HCPMMP-1.0 parcellation in :func:`mne.datasets.fetch_hcp_mmp_parcellation` by `Eric Larson`_
• Enable morphing between hemispheres with mne.compute_morph_matrix by `Christian Brodbeck`_
• Add return_residual to :func:`mne.minimum_norm.apply_inverse` by `Eric Larson`_
• Add return_drop_log to :func:`mne.preprocessing.compute_proj_eog` and :func:`mne.preprocessing.compute_proj_ecg` by `Eric Larson`_
• Add time cursor and category/amplitude status message into the single-channel evoked plot by `Jussi Nurminen`_

BUG

• Fixed a bug when creating spherical volumetric grid source spaces in :func:`setup_volume_source_space` by improving the minimum-distance computations, which in general will decrease the number of used source space points by `Eric Larson`_
• Fix bug in :meth:`mne.io.read_raw_brainvision` read .vhdr files with ANSI codepage by `Okba Bekhelifi`_ and `Alex Gramfort`_
• Fix unit scaling when reading in EGI digitization files using mne.channels.read_dig_montage by `Matt Boggess`_
• Fix picks default in :meth:`mne.io.Raw.filter` to include ref_meg channels by default by `Eric Larson`_
• Fix :class:`mne.decoding.CSP` order of spatial filter in patterns_ by `Alexandre Barachant`_
• :meth:`mne.concatenate_epochs` now maintains the relative position of events during concatenation by `Alexandre Barachant`_
• Fix bug in script mne make_scalp_surfaces by `Denis Engemann`_ (this bug prevented creation of high-resolution meshes when they were absent in the first place.)
• Fix writing of raw files with empty set of annotations by `Jaakko Leppakangas`_
• Fix bug in :meth:`mne.preprocessing.ICA.plot_properties` where merging gradiometers would fail by `Jaakko Leppakangas`_
• Fix :func:`mne.viz.plot_sensors` to maintain proper aspect ratio by `Eric Larson`_
• Fix :func:`mne.viz.plot_topomap` to allow 0 contours by `Jaakko Leppakangas`_
• Fix :class:`mne.preprocessing.ICA` source-picking to increase threshold for rank estimation to 1e-14 by `Jesper Duemose Nielsen`_
• Fix :func:`mne.set_bipolar_reference` to support duplicates in anodes by `Jean-Baptiste Schiratti`_ and `Alex Gramfort`_
• Fix visuals of :func:`mne.viz.plot_evoked` and a bug where ylim changes when using interactive topomap plotting by `Jaakko Leppakangas`_
• Fix :meth:`mne.Evoked.plot_topomap` when using the mask argument with paired gradiometers by `Eric Larson`_
• Fix bug in :meth:`mne.Label.fill` where an empty label raised an error, by `Eric Larson`_
• Fix :func:`mne.io.read_raw_ctf` to also include the samples in the last block by `Jaakko Leppakangas`_
• Fix :meth:`mne.preprocessing.ICA.save` to close file before attempting to delete it when write fails by `Jesper Duemose Nielsen`_
• Fix :func:`mne.simulation.simulate_evoked` to use nave parameter instead of snr, by `Yousra Bekhti`_
• Fix :func:`mne.read_bem_surfaces` for BEM files missing normals by `Christian Brodbeck`_
• Fix :func:`mne.transform_surface_to` to actually copy when copy=True by `Eric Larson`_
• Fix :func:`mne.io.read_raw_brainvision` to read vectorized data correctly by `Jaakko Leppakangas`_ and `Phillip Alday`_
• Fix mne.connectivity.spectral_connectivity so that if n_jobs > 1 it does not ignore last n_epochs % n_jobs epochs by `Mikołaj Magnuski`_
• Fix :func:`mne.io.read_raw_edf` to infer sampling rate correctly when reading EDF+ files where tal-channel has a higher sampling frequency by `Jaakko Leppakangas`_
• Fix default value of kind='topomap' in mne.channels.Montage.plot to be consistent with :func:`mne.viz.plot_montage` by `Clemens Brunner`_
• Fix bug in :meth:`to_data_frame <mne.io.Raw.to_data_frame>` where non-consecutive picks would make the function crash by `Jaakko Leppakangas`_
• Fix channel picking and drop in :class:`mne.time_frequency.EpochsTFR` by `Lukáš Hejtmánek`_
• Fix :func:`mne.SourceEstimate.transform` to properly update :attr:`mne.SourceEstimate.times` by `Marijn van Vliet`_
• Fix :func:`mne.viz.plot_evoked_joint` to allow custom titles without appending information about the channels by `Jaakko Leppakangas`_
• Fix writing a forward solution after being processed by :func:`mne.forward.restrict_forward_to_label` or :func:`mne.forward.restrict_forward_to_stc` by `Marijn van Vliet`_
• Fix bug in :func:`mne.viz.plot_compare_evokeds` where truncate_yaxis was ignored (default is now False), by `Jona Sassenhagen`_
• Fix bug in :func:`mne.viz.plot_evoked` where all xlabels were removed when using spatial_colors=True, by `Jesper Duemose Nielsen`_
• Fix field mapping :func:`mne.make_field_map` and MEG bad channel interpolation functions (e.g., :meth:`mne.Evoked.interpolate_bads`) to choose a better number of components during pseudoinversion when few channels are available, by `Eric Larson`_
• Fix bug in :func:`mne.io.read_raw_brainvision`, changed default to read coordinate information if available and added test, by `Jesper Duemose Nielsen`_
• Fix bug in :meth:`mne.SourceEstimate.to_original_src` where morphing failed if two vertices map to the same target vertex, by `Marijn van Vliet`_
• Fix :class:`mne.preprocessing.Xdawn` to give verbose error messages about rank deficiency and handle transforming :class:`mne.Evoked`, by `Eric Larson`_
• Fix bug in DC and Nyquist frequency multitaper PSD computations, e.g. in mne.time_frequency.psd_multitaper, by `Eric Larson`_
• Fix default padding type for :meth:`mne.Epochs.resample` and :meth:`mne.Evoked.resample` to be 'edge' by default, by `Eric Larson`_
• Fix :func:`mne.inverse_sparse.mixed_norm`, :func:`mne.inverse_sparse.tf_mixed_norm` and :func:`mne.inverse_sparse.gamma_map` to work with volume source space and sphere head models in MEG by `Alex Gramfort`_ and `Yousra Bekhti`_
• Fix :meth:`mne.Evoked.as_type` channel renaming to append '_v' instead of '_virtual' to channel names to comply with shorter naming (15 char) requirements, by `Eric Larson`_
• Fix treatment of CTF HPI coils as fiducial points in :func:`mne.gui.coregistration` by `Eric Larson`_
• Fix resampling of events along with raw in :func:`mne.io.Raw` to now take into consideration the value of first_samp by `Chris Bailey`_
• Fix labels of PSD plots in :func:`mne.viz.plot_raw_psd` by `Alejandro Weinstein`_
• Fix depth weighting of sparse solvers (:func:`mne.inverse_sparse.mixed_norm`, :func:`mne.inverse_sparse.tf_mixed_norm` and :func:`mne.inverse_sparse.gamma_map`) with free orientation source spaces to improve orientation estimation by `Alex Gramfort`_ and `Yousra Bekhti`_
• Fix the threshold in :func:`mne.beamformer.rap_music` to properly estimate the rank by `Yousra Bekhti`_
• Fix treatment of vector inverse in :func:`mne.minimum_norm.apply_inverse_epochs` by `Emily Stephen`_
• Fix :func:`mne.find_events` when passing a list as stim_channel parameter by `Alex Gramfort`_
• Fix parallel processing when computing covariance with shrinkage estimators by `Denis Engemann`_

API

• Removed the mne.datasets.megsim dataset because it was taken down by its host (MRN). Use the :mod:`mne.simulation` functions instead, by `Eric Larson`_
• Add skip_by_annotation to :meth:`mne.io.Raw.filter` to process data concatenated with e.g. :func:`mne.concatenate_raws` separately. This parameter will default to the old behavior (treating all data as a single block) in 0.15 but will change to skip_by_annotation='edge', which will separately filter the concatenated chunks separately, in 0.16. This should help prevent potential problems with filter-induced ringing in concatenated files, by `Eric Larson`_
• ICA channel names have now been reformatted to start from zero, e.g. "ICA000", to match indexing schemes in :class:`mne.preprocessing.ICA` and related functions, by `Stefan Repplinger`_ and `Eric Larson`_
• Add :func:`mne.beamformer.make_lcmv` and :func:`mne.beamformer.apply_lcmv`, :func:`mne.beamformer.apply_lcmv_epochs`, and :func:`mne.beamformer.apply_lcmv_raw` to enable the separate computation and application of LCMV beamformer weights by `Britta Westner`_, `Alex Gramfort`_, and `Denis Engemann`_.
• Add weight_norm parameter to enable both unit-noise-gain beamformer and neural activity index (weight normalization) and make whitening optional by allowing noise_cov=None in mne.beamformer.lcmv, mne.beamformer.lcmv_epochs, and mne.beamformer.lcmv_raw, by `Britta Westner`_, `Alex Gramfort`_, and `Denis Engemann`_.
• Add new filtering mode fir_design='firwin' (default in the next 0.16 release) that gets improved attenuation using fewer samples compared to fir_design='firwin2' (default in the current 0.15 release) by `Eric Larson`_
• Make the goodness of fit (GOF) of the dipoles returned by :func:`mne.beamformer.rap_music` consistent with the GOF of dipoles returned by :func:`mne.fit_dipole` by `Alex Gramfort`_.
• :class:`mne.decoding.SlidingEstimator` will now replace mne.decoding.TimeDecoding to make it generic and fully compatible with scikit-learn, by `Jean-Rémi King`_ and `Alex Gramfort`_
• :class:`mne.decoding.GeneralizingEstimator` will now replace mne.decoding.GeneralizationAcrossTime to make it generic and fully compatible with scikit-learn, by `Jean-Rémi King`_ and `Alex Gramfort`_
• mne.viz.decoding.plot_gat_times, mne.viz.decoding.plot_gat_matrix are now deprecated. Use matplotlib instead as shown in the examples, by `Jean-Rémi King`_ and `Alex Gramfort`_
• Add norm_trace parameter to control single-epoch covariance normalization in :class:`mne.decoding.CSP`, by `Jean-Rémi King`_
• Allow passing a list of channel names as show_names in function :func:`mne.viz.plot_sensors` and methods :meth:`mne.Evoked.plot_sensors`, :meth:`mne.Epochs.plot_sensors` and :meth:`mne.io.Raw.plot_sensors` to show only a subset of channel names by `Jaakko Leppakangas`_
• Make function mne.io.eeglab.read_events_eeglab public to allow loading overlapping events from EEGLAB files, by `Jona Sassenhagen`_.
• :func:`mne.find_events` mask_type parameter will change from 'not_and' to 'and' in 0.16.
• Instead of raising an error, duplicate channel names in the data file are now appended with a running number by `Jaakko Leppakangas`_
• :func:`mne.io.read_raw_edf` has now 'auto' option for stim_channel (default in version 0.16) that automatically detects if EDF annotations or GDF events exist in the header and constructs the stim channel based on these events by `Jaakko Leppakangas`_
• :meth:`mne.io.Raw.plot_psd` now rejects data annotated bad by default. Turn off with reject_by_annotation=False, by `Eric Larson`_
• :func:`mne.set_eeg_reference` and the related methods (e.g., :meth:`mne.io.Raw.set_eeg_reference`) have a new argument projection, which if set to False directly applies an average reference instead of adding an SSP projector, by `Clemens Brunner`_
• Deprecate plot_trans in favor of :func:`mne.viz.plot_alignment` and add bem parameter for plotting conductor model by `Jaakko Leppakangas`_
• mne.beamformer.tf_lcmv now has a raw parameter to accommodate epochs objects that already have data loaded with preload=True, with :meth:`mne.Epochs.load_data`, or that are read from disk, by `Eric Larson`_
• mne.time_frequency.psd_welch and :func:`mne.time_frequency.psd_array_welch` now use a Hamming window (instead of a Hann window) by `Clemens Brunner`_
• picks parameter in mne.beamformer.lcmv, mne.beamformer.lcmv_epochs, mne.beamformer.lcmv_raw, mne.beamformer.tf_lcmv and :func:`mne.beamformer.rap_music` is now deprecated and will be removed in 0.16, by `Britta Westner`_, `Alex Gramfort`_, and `Denis Engemann`_.
• The keyword argument frequencies has been deprecated in favor of freqs in various time-frequency functions, e.g. :func:`mne.time_frequency.tfr_array_morlet`, by `Eric Larson`_
• Add patterns=False parameter in :class:`mne.decoding.ReceptiveField`. Turn on to compute inverse model coefficients, by `Nicolas Barascud`_
• The scale, scale_time, and unit parameters have been deprecated in favor of scalings, scalings_time, and units in :func:`mne.viz.plot_evoked_topomap` and related functions, by `Eric Larson`_
• loose parameter in inverse solvers has now a default value 'auto' depending if the source space is a surface, volume, or discrete type by `Alex Gramfort`_ and `Yousra Bekhti`_
• The behavior of 'mean_flip' label-flipping in :meth:`mne.extract_label_time_course` and related functions has been changed such that the flip, instead of having arbitrary sign, maximally aligns in the positive direction of the normals of the label, by `Eric Larson`_
• Deprecate force_fixed and surf_ori in :func:`mne.read_forward_solution` by `Daniel Strohmeier`_
• :func:`mne.convert_forward_solution` has a new argument use_cps, which controls whether information on cortical patch statistics is applied while generating surface-oriented forward solutions with free and fixed orientation by `Daniel Strohmeier`_
• :func:`mne.write_forward_solution` writes a forward solution as a forward solution with free orientation in X/Y/Z RAS coordinates if it is derived from a forward solution with free orientation and as a forward solution with fixed orientation in surface-based local coordinates otherwise by `Daniel Strohmeier`_
• loose=None in inverse solvers is deprecated, use explicitly loose=0 for fixed constraint and loose=1.0 for free orientations by `Eric Larson`_
• Zero-channel-value in PSD calculation in :func:`mne.viz.plot_raw_psd` has been relaxed from error to warning by `Alejandro Weinstein`_
• Expose "rank" parameter in :func:`mne.viz.plot_evoked_white` to correct rank estimates on the spot during visualization by `Denis Engemann`_, `Eric Larson`_, `Alex Gramfort`_.
• Show channel name under mouse cursor on topography plots by `Jussi Nurminen`_
• Return maximum response amplitude from :meth:`mne.Evoked.get_peak`

Authors

People who contributed to this release (in alphabetical order):

• akshay0724
• Alejandro Weinstein
• Alexander Rudiuk
• Alexandre Barachant
• Alexandre Gramfort
• Andrew Dykstra
• Britta Westner
• Chris Bailey
• Chris Holdgraf
• Christian Brodbeck
• Christopher Holdgraf
• Clemens Brunner
• Cristóbal Moënne-Loccoz
• Daniel McCloy
• Daniel Strohmeier
• Denis A. Engemann
• Emily P. Stephen
• Eric Larson
• Fede Raimondo
• Jaakko Leppakangas
• Jean-Baptiste Schiratti
• Jean-Rémi King
• Jesper Duemose Nielsen
• Joan Massich
• Jon Houck
• Jona Sassenhagen
• Jussi Nurminen
• Laetitia Grabot
• Laura Gwilliams
• Luke Bloy
• Lukáš Hejtmánek
• Mainak Jas
• Marijn van Vliet
• Mathurin Massias
• Matt Boggess
• Mikolaj Magnuski
• Nicolas Barascud
• Nicole Proulx
• Phillip Alday
• Ramonapariciog Apariciogarcia
• Robin Tibor Schirrmeister
• Rodrigo Hübner
• 19. 13. Gutstein
• Simon Kern
• Teon Brooks
• Yousra Bekhti