Version 0.14 (2017-03-24)

Changelog

• Add example of time-frequency decoding with CSP by Laura Gwilliams

• Automatically create a legend in mne.viz.plot_evoked_topo() by Jussi Nurminen

• Add I/O support for Artemis123 infant/toddler MEG data by Luke Bloy

• Add filter plotting functions mne.viz.plot_filter() and mne.viz.plot_ideal_filter() as well as filter creation function mne.filter.create_filter() by Eric Larson

• Add HCP-MMP1.0 parcellation dataset downloader by Eric Larson

• Add option to project EEG electrodes onto the scalp in mne.viz.plot_trans by Eric Larson

• Add option to plot individual sensors in mne.io.Raw.plot_psd() by Alex Gramfort and Eric Larson

• Add option to plot ECoG electrodes in mne.viz.plot_trans by Eric Larson

• Add convenient default values to mne.io.Raw.apply_hilbert() and mne.io.Raw.apply_function() by Denis Engemann

• Remove MNE-C requirement for mne make_scalp_surfaces by Eric Larson

• Add support for FastTrack Polhemus .mat file outputs in hsp argument of mne.channels.read_dig_montage by Eric Larson

• Add option to convert 3d electrode plots to a snapshot with 2d electrode positions with mne.viz.snapshot_brain_montage() by Chris Holdgraf

• Add skull surface plotting option to mne.viz.plot_trans by Jaakko Leppakangas

• Add minimum-phase filtering option in mne.io.Raw.filter() by Eric Larson

• Add support for reading ASCII BrainVision files in mne.io.read_raw_brainvision() by Eric Larson

• Add method of ICA objects for retrieving the component maps mne.preprocessing.ICA.get_components() by Jona Sassenhagen

• Add option to plot events in mne.viz.plot_epochs() by Jaakko Leppakangas

• Add dipole definitions for older phantom at Otaniemi in mne.dipole.get_phantom_dipoles() by Eric Larson

• Add spatial colors option for mne.viz.plot_raw_psd() by Jaakko Leppakangas

• Add functions like get_volume_labels_from_src() to handle mixed source spaces by Annalisa Pascarella

• Add convenience function for opening MNE documentation open_docs() by Eric Larson

• Add option in mne.io.Raw.plot() to display the time axis relative to raw.first_samp by Mainak Jas

• Add new mne.datasets.visual_92_categories dataset by Jaakko Leppakangas

• Add option in mne.io.read_raw_edf() to allow channel exclusion by Jaakko Leppakangas

• Allow integer event codes in mne.read_epochs_eeglab() by Jaakko Leppakangas

• Add ability to match channel names in a case insensitive manner when applying a mne.channels.Montage by Marijn van Vliet

• Add yscale keyword argument to mne.time_frequency.AverageTFR.plot() that allows specifying whether to present the frequency axis in linear ('linear') or log ('log') scale. The default value is 'auto' which detects whether frequencies are log-spaced and sets yscale to log. Added by Mikołaj Magnuski

• Add Representational Similarity Analysis (RSA) example on mne.datasets.visual_92_categories.data_path dataset by Jaakko Leppakangas, Jean-Rémi King and Alex Gramfort

• Add support for NeuroScan files with event type 3 in mne.io.read_raw_cnt() by Marijn van Vliet

• Add interactive annotation mode to mne.io.Raw.plot() (accessed by pressing ‘a’) by Jaakko Leppakangas

• Add support for deleting all projectors or a list of indices in mne.io.Raw.del_proj() by Eric Larson

• Add source space plotting with mne.SourceSpaces.plot() using mne.viz.plot_trans by Eric Larson

• Add mne.decoding.get_coef() to retrieve and inverse the coefficients of a linear model - typically a spatial filter or pattern, by Jean-Rémi King

• Add support for reading in EGI MFF digitization coordinate files in mne.channels.read_dig_montage by Matt Boggess

• Add n_per_seg keyword argument to mne.time_frequency.psd_welch and mne.time_frequency.psd_array_welch() that allows to control segment length independently of n_fft and use zero-padding when n_fft > n_per_seg by Mikołaj Magnuski

• Add annotation aware data getter mne.io.Raw.get_data() by Jaakko Leppakangas

• Add support of dipole location visualization with MRI slice overlay with matplotlib to mne.viz.plot_dipole_locations() via mode=’orthoview’ parameter by Jaakko Leppakangas and Alex Gramfort

• Add plotting of head positions as a function of time in mne.viz.plot_head_positions() by Eric Larson

• Add real_filter option to mne.beamformer.dics, mne.beamformer.dics_source_power, mne.beamformer.tf_dics and mne.beamformer.dics_epochs by Eric Larson, Alex Gramfort and Andrea Brovelli.

• Add a demo script showing how to use a custom inverse solver with MNE by Alex Gramfort

• Functions mne.preprocessing.create_ecg_epochs(), mne.preprocessing.create_eog_epochs(), mne.compute_raw_covariance() and ICA methods mne.preprocessing.ICA.score_sources(), mne.preprocessing.ICA.find_bads_ecg(), mne.preprocessing.ICA.find_bads_eog() are now annotation aware by Jaakko Leppakangas

• Allow using spatial_colors for non-standard layouts by creating custom layouts from channel locations and add to_sphere keyword to mne.viz.plot_sensors() to allow plotting sensors that are not on the head surface by Jaakko Leppakangas

• Concatenating raws with mne.concatenate_raws() now creates boundary annotations automatically by Jaakko Leppakangas

• mne.viz.plot_projs_topomap() now supports plotting EEG topomaps by passing in mne.Info by Eric Larson

BUG

• Fix bug with DICS and LCMV (e.g., mne.beamformer.lcmv, mne.beamformer.dics) where regularization was done improperly. The default reg=0.01 has been changed to reg=0.05, by Andrea Brovelli, Alex Gramfort, and Eric Larson

• Fix callback function call in mne.viz.topo._plot_topo_onpick by Erkka Heinila

• Fix reading multi-file CTF recordings in mne.io.read_raw_ctf() by Niklas Wilming

• Fix computation of AR coefficients across channels in mne.time_frequency.fit_iir_model_raw() by Eric Larson

• Fix maxfilter channel names extra space bug in mne.preprocessing.maxwell_filter() by Sheraz Khan

• mne.channels.find_layout() now leaves out the excluded channels by Jaakko Leppakangas

• Array data constructors mne.io.RawArray and EvokedArray now make a copy of the info structure by Jaakko Leppakangas

• Fix bug with finding layouts in mne.viz.plot_projs_topomap() by Eric Larson

• Fix bug mne.io.anonymize_info() when Info does not contain ‘file_id’ or ‘meas_id’ fields by Jean-Rémi King

• Fix colormap selection in mne.viz.plot_evoked_topomap() when using positive vmin with negative data by Jaakko Leppakangas

• Fix channel name comparison in mne.channels.read_montage so that if ch_names is provided, the returned montage will have channel names in the same letter case by Jaakko Leppakangas

• Fix inst.set_montage(montage) to only set inst.info['dev_head_t'] if dev_head_t=True in mne.channels.read_dig_montage by Eric Larson

• Fix handling of events in mne.realtime.RtEpochs when the triggers were split between two buffers resulting in missing and/or duplicate epochs by Mainak Jas and Antti Rantala

• Fix bug with automatic decimation in mne.io.read_raw_kit() by Keith Doelling

• Fix bug with setup_volume_source_space() where arguments subject and subjects_dir were ignored by Jaakko Leppakangas

• Fix sanity check for incompatible threshold and tail values in clustering functions like mne.stats.spatio_temporal_cluster_1samp_test() by Eric Larson

• Fix _bad_dropped not being set when loading eeglab epoched files via mne.read_epochs_eeglab() which resulted in len() not working by Mikołaj Magnuski

• Fix a bug in mne.time_frequency.AverageTFR.plot() when plotting without a colorbar by Jaakko Leppakangas

• Fix _filenames attribute in creation of mne.io.RawArray with mne.preprocessing.ICA.get_sources() by Paul Pasler

• Fix contour levels in mne.viz.plot_evoked_topomap() to be uniform across topomaps by Jaakko Leppakangas

• Fix bug in mne.preprocessing.maxwell_filter() where fine calibration indices were mismatched leading to an AssertionError by Eric Larson

• Fix bug in mne.preprocessing.fix_stim_artifact() where non-data channels were interpolated by Eric Larson

• mne.decoding.Scaler now scales each channel independently using data from all time points (epochs and times) instead of scaling all channels for each time point. It also now accepts parameter scalings to determine the data scaling method (default is None to use static channel-type-based scaling), by Asish Panda, Jean-Rémi King, and Eric Larson

• Raise error if the cv parameter of mne.decoding.GeneralizationAcrossTime and mne.decoding.TimeDecoding is not a partition and the predict_mode is “cross-validation” by Jean-Rémi King

• Fix bug in mne.io.read_raw_edf() when preload=False and channels have different sampling rates by Jaakko Leppakangas

• Fix mne.read_labels_from_annot() to set label.values[:]=1 rather than 0 for consistency with the Label class by Jon Houck

• Fix plotting non-uniform freqs (for example log-spaced) in mne.time_frequency.AverageTFR.plot() by Mikołaj Magnuski

• Fix mne.minimum_norm.compute_source_psd() when used with pick_ori=None by Annalisa Pascarella and Alex Gramfort

• Fix bug in mne.Annotations where concatenating two raws where orig_time of the second run is None by Jaakko Leppakangas

• Fix reading channel location from eeglab .set files when some of the channels do not provide this information. Previously all channel locations were ignored in such case, now they are read - unless a montage is provided by the user in which case only channel names are read from set file. By Mikołaj Magnuski

• Fix reading eeglab .set files when .chanlocs structure does not contain X, Y or Z fields by Mikołaj Magnuski

• Fix bug with mne.simulation.simulate_raw() when interp != 'zero' by Eric Larson

• Fix mne.fit_dipole() to handle sphere model rank deficiency properly by Alex Gramfort

• Raise error in mne.concatenate_epochs() when concatenated epochs have conflicting event_id by Mikołaj Magnuski

• Fix handling of n_components=None in mne.preprocessing.ICA by Richard Höchenberger

• Fix reading of fiducials correctly from CTF data in mne.io.read_raw_ctf() by Jaakko Leppakangas

• Fix mne.beamformer.rap_music() to return dipoles with amplitudes in Am instead of nAm by Jaakko Leppakangas

• Fix computation of duality gap in mne.inverse_sparse.mxne_optim.dgap_l21 by Mathurin Massias

API

• The filtering functions band_pass_filter, band_stop_filter, low_pass_filter, and high_pass_filter have been deprecated in favor of mne.filter.filter_data() by Eric Larson

• EvokedArray now has default value tmin=0. by Jaakko Leppakangas

• The ch_type argument for mne.viz.plot_trans has been deprecated, use eeg_sensors and meg_sensors instead, by Eric Larson

• The default tmax=60. in mne.io.Raw.plot_psd() will change to tmax=np.inf in 0.15, by Eric Larson

• Base classes mne.io.BaseRaw and mne.BaseEpochs are now public to allow easier typechecking, by Daniel McCloy

• mne.io.read_raw_edf() now combines triggers from multiple tal channels to ‘STI 014’ by Jaakko Leppakangas

• The measurement info Info no longer contains a potentially misleading info['filename'] entry. Use class properties like mne.io.Raw.filenames or mne.Epochs.filename instead by Eric Larson

• Default fiducial name change from ‘nz’ to ‘nasion’ in mne.channels.read_montage, so that it is the same for both mne.channels.Montage and :class: mne.channels.DigMontage by Leonardo Barbosa

• MNE’s additional files for the fsaverage head/brain model are now included in MNE-Python, and the now superfluous mne_root parameter to create_default_subject() has been deprecated by Christian Brodbeck

• An overwrite=False default parameter has been added to write_source_spaces() to protect against accidental overwrites, by Eric Larson

• The mne.decoding.LinearModel class will no longer support plot_filters and plot_patterns, use mne.EvokedArray with mne.decoding.get_coef() instead, by Jean-Rémi King

• Made functions mne.time_frequency.tfr_array_multitaper(), mne.time_frequency.tfr_array_morlet(), mne.time_frequency.tfr_array_stockwell(), mne.time_frequency.psd_array_multitaper() and mne.time_frequency.psd_array_welch() public to allow computing TFRs and PSDs on numpy arrays by Jaakko Leppakangas

• mne.preprocessing.ICA.fit() now rejects data annotated bad by default. Turn off with reject_by_annotation=False, by Jaakko Leppakangas

• mne.io.read_raw_egi() now names channels with pattern ‘E<idx>’. This behavior can be changed with parameter channel_naming by Jaakko Leppakangas

• the name parameter in mne.Epochs is deprecated, by Jaakko Leppakangas

Authors

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

• Alexander Rudiuk

• Alexandre Gramfort

• Annalisa Pascarella

• Antti Rantala

• Asish Panda

• Burkhard Maess

• Chris Holdgraf

• Christian Brodbeck

• Cristóbal Moënne-Loccoz

• Daniel McCloy

• Denis A. Engemann

• Eric Larson

• Erkka Heinila

• Hermann Sonntag

• Jaakko Leppakangas

• Jakub Kaczmarzyk

• Jean-Rémi King

• Jon Houck

• Jona Sassenhagen

• Jussi Nurminen

• Keith Doelling

• Leonardo S. Barbosa

• Lorenz Esch

• Lorenzo Alfine

• Luke Bloy

• Mainak Jas

• Marijn van Vliet

• Matt Boggess

• Matteo Visconti

• Mikolaj Magnuski

• Niklas Wilming

• Paul Pasler

• Richard Höchenberger

• Sheraz Khan

• Stefan Repplinger

• Teon Brooks

• Yaroslav Halchenko