What’s new

Version 0.21.3

Bugs

• Fix bug in mne.io.read_raw_kit() where scale factors for EEG channels could be set to zero (#8542 by Eric Larson)

Version 0.21.2

Bugs

• Add option to disable TQDM entirely with MNE_TQDM='off' (#8515 by Eric Larson)

• Fix reading GDF files with excluded channels in mne.io.read_raw_gdf() (#8520 by Clemens Brunner)

• Fix bug in mne.preprocessing.compute_fine_calibration() where the magnetometer calibration coefficients were computed incorrectly (#8522 by Eric Larson)

• Fix bug in mne.preprocessing.Xdawn tests by Eric Larson (#8496)

Version 0.21.1

Bugs

• Fix bug with mne.io.egi.tests/test_egi.py where it mandatorily downloaded testing data when it was not necessary by new contributor Aniket Pradhan (#8474)

• Fix bug with reading split files that have dashes in the filename by new contributor Eduard Ort (#8339)

• Fix bug with mne.io.Raw.save() when using split_naming='bids' where non-split files would still be named name_split-01_meg.fif instead of the requested name_meg.fif by Alex Gramfort and Eric Larson (#8464)

• Fix bug with mne.viz.plot_source_estimates() when using the PyVista backend where singleton time points were not handled properly by Eric Larson (#8285)

• Fix bug with compensated CTF data when picking channels without preload by Eric Larson (#8318)

• Fix bug when passing axes to plotting functions, matplotlib.pyplot.tight_layout() will not be called when the figure was created using a constrained layout by Eric Larson (#8344)

• Fix bug when merging fNIRS channels in mne.viz.plot_evoked_topomap() and related functions by Robert Luke (#8306)

• mne.io.read_raw_edf() now supports EDF files with invalid recording dates by Clemens Brunner (#8283)

• Fix missing documentation of mne.io.read_raw_nihon() in Importing data from EEG devices by Adam Li (:gh`8320`)

• Fix bug with mne.add_reference_channels() when mne.io.Raw.reorder_channels() or related methods are used afterward by Eric Larson (#8303, ##8484)

• Fix bug where the verbose arguments to mne.Evoked.apply_baseline() and mne.Epochs.apply_baseline() were not keyword-only by Eric Larson (#8349)

• Fix bug that plot_ica_overlay would sometimes not create red traces, by Richard Höchenberger (#8341)

• Pass rank everyhwere in forward preparation for source imaging. This bug affected sparse solvers when using maxfilter data, by Alex Gramfort (#8368)

• Fix bug in mne.viz.plot_alignment() where ECoG and sEEG channels were not plotted and fNIRS channels were always plotted in the head coordinate frame by Eric Larson (#8393)

• Fix bug in mne.set_bipolar_reference() where ch_info could contain invalid channel information keys by Eric Larson

• Fix bug in mne.viz.plot_source_estimates(), which wouldn’t accept the valid parameter value backend='pyvista', by Guillaume Favelier

• Attempting to remove baseline correction from preloaded Epochs will now raise an exception by Richard Höchenberger (#8435)

• When reading BrainVision raw data, the channel units and types were sometimes not inferred correctly by Richard Höchenberger (#8434)

Version 0.21

Enhancements

• Modified mne.Epochs.pick_types() to remove dropped channel types from reject and flat dictionaries by new contributor Rahul Nadkarni

• Add function 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 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 mne.io.read_raw_brainvision() and provided as a .impedances attribute of raw by new contributor Jan Sedivy and Stefan Appelhoff

• Add function 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, 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 Source alignment and coordinate frames tutorial, by Alex Rockhill

• Improve memory efficiency of mne.concatenate_epochs() by Eric Larson

• Allow picking channels in raw instances (e.g., mne.io.Raw.pick_types()) without preloading data, by Eric Larson

• mne.preprocessing.ICA.plot_sources() now plots annotation markers similar to mne.io.Raw.plot() by Luke Bloy

• Add support for scalar multiplication and division of mne.time_frequency.AverageTFR instances by Luke Bloy

• Add support for signals in mV for mne.io.read_raw_brainvision() by Clemens Brunner

• mne.Epochs.plot_psd_topomap() and 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 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 mne.MixedSourceEstimate.plot() and mne.VolSourceEstimate.plot_3d() by Eric Larson

• Add mne.MixedSourceEstimate.surface() and mne.MixedSourceEstimate.volume() methods to allow surface and volume extraction by Eric Larson

• Add mne.VectorSourceEstimate.project() to project vector source estimates onto the direction of maximum source power by Eric Larson

• Add support to mne.extract_label_time_course() for vector-valued and volumetric source estimates by Eric Larson

• Add method mne.VolSourceEstimate.in_label() by Eric Larson

• Add support for mixed source spaces to mne.compute_source_morph() by Eric Larson

• Add support for volume and mixed source spaces to 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 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 mne.compute_source_morph() by Eric Larson

• Add explained variance logging to mne.inverse_sparse.mixed_norm(), mne.inverse_sparse.gamma_map(), and mne.beamformer.rap_music() by Eric Larson

• Add tol_kind option to mne.compute_rank() by Eric Larson

• Allow resampling raw data with mne.io.Raw.resample() without preloading data, by Eric Larson

• Allow using pick_ori='vector' with a fixed-orientation inverse to facilitate visualization with mne.viz.plot_vector_source_estimates() by Eric Larson

• mne.viz.plot_dipole_locations() and 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 mne.viz.plot_dipole_locations() in 'orthoview' mode by Eric Larson

• Add temporal derivative distribution repair (TDDR) mne.preprocessing.nirs.temporal_derivative_distribution_repair() with shortened alias mne.preprocessing.nirs.tddr by Robert Luke

• Add 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 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 mne.io.Raw.interpolate_bads() and related functions with method=dict(eeg='MNE') by Eric Larson

• Added ability of mne.io.read_raw_nirx() to open data by passing path to header file Robert Luke

• Add mne.channels.DigMontage.rename_channels() to allow renaming montage channels by Eric Larson

• Document mne.channels.compute_native_head_t() to allow computing the native-to-head transformation that will be applied when doing raw.set_montage and related functions by Eric Larson

• Add support to in 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 mne.preprocessing.annotate_muscle_zscore() to annotate periods with muscle artifacts. by Adonay Nunes

• Add mne.stats.ttest_ind_no_p() to mirror 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 mne.io.read_raw_nirx() by Eric Larson

• Speed up mne.Epochs.copy() and mne.Epochs.__getitem__() by avoiding copying immutable attributes by Eric Larson

• Speed up and reduce memory usage of mne.SourceEstimate.plot() and related functions/methods when show_traces=True by Eric Larson

• Reduce memory usage of plot_psd, psd_welch, and 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 mne.viz.plot_bem() by Eric Larson

• Add mne.viz.centers_to_edges() to help when using matplotlib.axes.Axes.pcolormesh() with flat shading by Eric Larson

• Add on_missing='raise' to mne.io.Raw.set_montage() and related functions to allow ignoring of missing electrode coordinates by Adam Li

• Add on_missing='raise' to mne.viz.plot_events() to allow ignoring missing events when passing event_id by Eric Larson

• Add REST EEG infinity reference scheme to 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 mne.preprocessing.ICA by Eric Larson

• Add plot option to 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 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 mne.viz.plot_evoked_white(), mne.Evoked.plot_white(), and mne.viz.plot_snr_estimate() by Eric Larson

• Change default to surfaces='auto' from surfaces='head' to allow mne.viz.plot_alignment() to work when just passing a mne.Info as plot_alignment(info) by Eric Larson

• Add ECoG misc EDF dataset to the Working with ECoG data tutorial to show snapshots of time-frequency activity by Adam Li

• Add mne.viz.set_3d_options() and MNE_3D_OPTION_ANTIALIAS environment variable to control full-scene antialiasing (FXAA) in 3D functions like mne coreg, mne.viz.plot_alignment(), and 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 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 mne.beamformer.make_dics() by Marijn van Vliet

• Add better error message when trying to save incompatible 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 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 mne.io.Raw.fix_mag_coil_types() to mne.preprocessing.maxwell_filter() by Eric Larson

• Add extended SSS (eSSS) support to mne.preprocessing.maxwell_filter() by Eric Larson

• Add 'auto' option to 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 mne.viz.set_3d_backend() by Guillaume Favelier

• Add support for reading and writing surfaces in Wavefront .obj format to the mne.read_surface() and 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

• mne.write_evokeds() will now accept 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 mne.io.read_raw_kit() by Alex Gramfort and Eric Larson

• The reject_tmin and reject_tmax parameters of mne.Epochs are now taken into account when using the reject_by_annotation parameter by Stefan Appelhoff

• 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 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 mne.write_bem_surfaces() and mne.write_bem_solution() by Eric Larson

• When picking a subset of channels, or when dropping channels from Raw, Epochs, or Evoked, projectors that can only be applied to the removed channels will now be dropped automatically by Richard Höchenberger

• 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 Evoked objects to 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 mne.stats.summarize_clusters_stc() using Numba by Yu-Han Luo

• Add reject_by_annotation=True to mne.make_fixed_length_epochs() and mne.preprocessing.ICA.plot_properties() to reject bad data segments based on annotation by Yu-Han Luo

• parse_folder now accepts a path-like folder name (it used to work with strings only) by Alex Gramfort

• Add component_order parameter to 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 mne.SourceSpaces and mne.SourceEstimate and related classes by Eric Larson

• Add reader for Persyst (.lay + .dat format) data in 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 mne.io.read_raw_snirf() by Robert Luke

• Evoked has gained tmin and tmax attributes for more consistency with Epochs by Richard Höchenberger

Bugs

• Fix bug for writing and reading complex evoked data modifying mne.write_evokeds() and 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 mne.VolSourceEstimate.save() by new contributor Lau Møller Andersen

• Fix bug with logging in mne.io.Raw.set_eeg_reference() and related functions by new contributor Simeon Wong

• Fix bug with mne.io.read_raw_gdf() where birthdays were not parsed properly, leading to an error by new contributor Svea Marie Meyer

• Fix bug with mne.io.read_raw_edf() where recording ID was not read properly for non-ASCII characters by new contributor Lx37

• Fix bug in 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 mne.chpi.compute_chpi_amplitudes() and mne.chpi.filter_chpi() to optimize time window length by new contributor Steven Bierer

• Fix bug with 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 stc.project('nn', src) to be applied after stc was restricted to an mne.Label by Luke Bloy

• Fix bug with mne.io.Raw.set_meas_date() to support setting meas_date to None, by Luke Bloy

• Fix bug with 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 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 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 mne.preprocessing.annotate_movement() where bad data segments, specified in raw.annotations, would be handled incorrectly by Luke Bloy

• Fix bug with 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 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 mne.compute_source_morph() where outermost voxels in the destination source space could be errantly omitted by Eric Larson

• Fix bug with mne.compute_source_morph() where complex data was cast to real when doing a volumetric morph by Eric Larson

• Fix bug with mne.minimum_norm.compute_source_psd_epochs() and mne.minimum_norm.source_band_induced_power() raised errors when method='eLORETA' by Eric Larson

• Fix bug with mne.minimum_norm.apply_inverse() where the explained variance did not work for complex data by Eric Larson

• Fix bug with 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 mne.combine_evoked() where equal-weighted averages were wrongly computed as equal-weighted sums, by Daniel McCloy

• Fix bug with mne.channels.DigMontage.plot() when reference channels with no defined position are present, by Eric Larson

• Fix bug with 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 mne.inverse_sparse.mixed_norm() and mne.inverse_sparse.gamma_map() with return_as_dipoles=True and 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 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 mne.viz.plot_evoked_topomap() by Daniel McCloy

• Fix plotting with mne.viz.plot_evoked_topomap() to pre-existing axes by Daniel McCloy

• Fix bug with 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 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 mne.io.Raw.plot() and 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 mne.time_frequency.read_tfrs() where info['meas_date'] was not parsed correctly, by Eric Larson

• Fix bug with 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 mne.stats.spatio_temporal_cluster_1samp_test() by Eric Larson

• Fix handling of signs when using TFCE by Eric Larson

• The 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 VolSourceEstimate.vertices was an instance of ndarray instead of list of one ndarray, by Eric Larson

• Fix default to be foreground=None in 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 mne.time_frequency.AverageTFR.plot_joint() and mne.time_frequency.AverageTFR.plot_topo() by Eric Larson

• Fix bug with mne.io.Raw.plot() where toggling all projectors did not actually take effect by Eric Larson

• Fix bug with mne.write_proj() where the number of columns was incorrectly written by Eric Larson

• Fix bug with mne.read_epochs() when loading data in complex format with preload=False by Eric Larson

• Fix bug with mne.Epochs.save() where the file splitting calculations did not account for the sizes of non-data writes by Eric Larson

• Fix bug with mne.Epochs when metadata was not subselected properly when event_repeated='drop' by Eric Larson

• Fix bug with 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 mne.Report where the BEM section could not be toggled by Eric Larson

• Fix bug when using mne.Epochs.crop() to exclude the baseline period would break mne.Epochs.save() / 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 mne.viz.plot_bem() and mne.Report when plotting BEM contours when MRIs are not in standard FreeSurfer orientation by Eric Larson

• Fix bug with mne.minimum_norm.make_inverse_operator() where it would warn even when an explicit rank was used by Eric Larson

• Fix bugs with mne.beamformer.make_lcmv() and 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

  • mne.beamformer.apply_lcmv_cov() did not apply whitening and projections properly

• Fix 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 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 mne.Report() where unicode characters were not rendered properly (encoding for HTML was not set) by Eric Larson

• Fix bug with mne.preprocessing.nirs.scalp_coupling_index() where filter transition was incorrectly assigned by Robert Luke

• Fix bug with mne.make_forward_dipole() where mne.write_forward_solution() could not be used by Eric Larson

• Fix bug with mne.io.Raw.plot() when scalings='auto' where bad data would prevent channel plotting by Eric Larson

• Default border and extrapolate arguments for 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 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 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 mne.preprocessing.find_bad_channels_maxwell() where good data of exactly step duration would lead to an error by Eric Larson

• Fix bug with 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 mne.set_config() accept path-like input values by Richard Höchenberger

• Fix bug with mne.write_labels_to_annot() and 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 mne.beamformer.make_dics() where complex conjugates were not applied properly by Britta Westner and Eric Larson

• Fix bug with 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 mne.io.Raw.get_channel_types() and related methods where the ordering of picks was not preserved, by Eric Larson

• Fix bug with 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 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 mne.read_epochs_fieldtrip() when importing data without a trialinfo field by Thomas Hartmann

• Fix bug in mne.preprocessing.ICA.plot_properties() where time series plot doesn’t start at the proper tmin by Teon Brooks

• Fix bug with mne.preprocessing.ICA.plot_properties() where a mne.io.Raw object with annotations would lead to an error by Yu-Han Luo

• Fix bug with mne.events_from_annotations(raw.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 → find_ch_adjacency

  • mne.channels.read_ch_connectivity → read_ch_adjacency

  • mne.spatial_dist_connectivity → spatial_dist_adjacency

  • mne.spatial_inter_hemi_connectivity → spatial_inter_hemi_adjacency

  • mne.spatial_src_connectivity → spatial_src_adjacency

  • mne.spatial_tris_connectivity → spatial_tris_adjacency

  • mne.spatio_temporal_dist_connectivity → spatio_temporal_dist_adjacency

  • mne.spatio_temporal_src_connectivity → spatio_temporal_src_adjacency

  • mne.spatio_temporal_tris_connectivity → 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 mne.io.read_raw_kit() will change from True to False in 0.22, by Eric Larson

• The normalize_fwd argument of mne.beamformer.make_dics() has been deprecated in favor of depth, by Eric Larson

• The overwrite parameter of mne.write_bem_surfaces() and 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 mne.preprocessing.ICA.plot_scores() to allow plotting scores in multiple columns, by Luke Bloy

• In mne.stats.permutation_cluster_test() and 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 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 mne.Epochs.plot_psd_topomap() and mne.viz.plot_epochs_psd_topomap(); use new vlim parameter instead, by Daniel McCloy.

• The method stc_mixed.plot_surface for a mne.MixedSourceEstimate has been deprecated in favor of stc.surface().plot(...) by Eric Larson

• The method stc.normal for mne.VectorSourceEstimate has been deprecated in favor of stc.project('nn', src) by Eric Larson

• Add use_dev_head_trans parameter to 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 mne.channels.read_dig_captrak() to correct the spelling error: “captraCK” -> “captraK”, by Stefan Appelhoff

• The threshold argument in 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 mne.pick_types() will change to meg=False in version 0.22 by Clemens Brunner

• Added 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

Version 0.20

Changelog

• Improved mne.viz.plot_epochs() to label epoch counts starting from 0, by Sophie Herbst

• Add minimum_norm.apply_inverse_cov() to compute static power by applying inverse solutions to a data covariance matrix by Denis Engemann, Luke Bloy, and Eric Larson

• Add mne.minimum_norm.resolution_metrics() to compute various resolution metrics for inverse solutions, by Olaf Hauk

• Add current source density mne.preprocessing.compute_current_source_density() to compute the surface Laplacian in order to reduce volume conduction in data by Alex Rockhill

• Add mne.chpi.extract_chpi_locs_ctf() to extract cHPI coil locations from CTF data by Luke Bloy

• Add mne.chpi.compute_chpi_amplitudes(), mne.chpi.compute_chpi_locs(), and mne.chpi.compute_head_pos() to compute head positions from cHPI coil locations by Eric Larson and Luke Bloy

• Add allow_line_only option to mne.chpi.filter_chpi() to allow filtering line frequencies only in files that do not have cHPI information by Eric Larson

• Add mne.io.Raw.set_meas_date() by Eric Larson

• Add mne.Epochs.as_type() to allow remapping data in MEG channels to virtual magnetometer or gradiometer channels by Sophie Herbst and Alex Gramfort

• Add copy parameter to mne.Epochs.iter_evoked() by Alex Gramfort

• Add command mne setup_source_space to quickly set up bilateral hemisphere surface-based source space with subsampling by Victor Ferat.

• Add command mne sys_info to print system information by Eric Larson

• Add function mne.make_fixed_length_epochs() to segment raw into fixed length epochs by Mohammad Daneshzand

• Add support for computing patch information only in surface source space creation with add_dist='patch' in mne.setup_source_space() and dist_limit=0 in mne.add_source_space_distances() by Eric Larson

• Add mne.Label.restrict to restrict a label to vertices within a source space by Eric Larson

• Add support for passing a destination source space src_to in mne.compute_source_morph() to ensure morphing for multiple subjects results in consistent STCs, by Eric Larson

• Add support for smooth='nearest' for surfaces in mne.compute_source_morph() by Eric Larson

• Add support for plotting fNIRS channels in mne.viz.plot_alignment(), mne.viz.plot_evoked_topo() and mne.Evoked.animate_topomap() by Eric Larson and Robert Luke

• Add command line tool mne anonymize for anonymizing raw fiff files by Luke Bloy

• Add mne.preprocessing.find_bad_channels_maxwell() for automatic bad channel detection via Maxwell filtering by Eric Larson

• Add support to mne.io.anonymize_info() to allow time offset to be applied to dates by Luke Bloy

• Add support for computing resolution matrix to get point spread functions (PSF) and cross-talk functions (CTF) in mne.minimum_norm.make_inverse_resolution_matrix(), mne.beamformer.make_lcmv_resolution_matrix(), mne.minimum_norm.get_cross_talk(), mne.minimum_norm.get_point_spread() by Olaf Hauk

• Add mne.preprocessing.read_ica_eeglab() to read EEGLAB ICA decompositions by Christian O’Reilly

• Add keyboard functionality to interactive colorbar plotting TFRs by Stefan Repplinger

• Add the ability to return_event_id in mne.read_events() for use with MNE-C produced -annot.fif files, by Eric Larson

• Add option to mne.connectivity.spectral_connectivity() to compute corrected imaginary PLV by Adonay Nunes

• Add mne.SourceEstimate.estimate_snr() to estimate source-space SNR, by Kaisu Lankinen and Padma Sundaram

• Add option to specify the coordinate frame in mne.channels.read_custom_montage() by Eric Larson

• Add option to use match_case=False to mne.io.Raw.set_montage() and related functions by Eric Larson

• Add reader for NIRx data in mne.io.read_raw_nirx() by Robert Luke

• Add function to convert NIRS data to optical density mne.preprocessing.nirs.optical_density() by Robert Luke

• Add function to convert NIRS data to haemoglobin concentration mne.preprocessing.nirs.beer_lambert_law() by Robert Luke

• Add fig argument to mne.viz.plot_evoked_field() by Eric Larson

• Add functions to calculate spatial information of NIRS channels mne.preprocessing.nirs.source_detector_distances() and mne.preprocessing.nirs.short_channels() by Robert Luke

• Add reader for *.dat electrode position files mne.channels.read_dig_dat() by Christian Brodbeck

• Improved mne.viz.plot_events() to always show event counts by Eric Larson

• Improved LIMO Dataset usage and example for usage of mne.stats.linear_regression() by Jose Alanis

• Add support for reduce_rank=True for vector beamformers by Eric Larson

• Add method='sphere' support for using Freesurfer spherical inflation in mne.decimate_surface() to facilitate mesh downsampling for use with mne.make_bem_model() by Eric Larson

• Speed up mne.beamformer.make_lcmv() and mne.beamformer.make_dics() calculations by vectorizing linear algebra calls by Dmitrii Altukhov and Eric Larson

• Speed up mne.make_forward_solution() using Numba, by Eric Larson

• Speed up mne.io.read_raw_fif() data reading when the recording is long and there are many data tags repeatedly accessed, by Eric Larson

• For KIT systems without built-in layout, mne.channels.find_layout() now falls back on an automatically generated layout, by Christian Brodbeck

• mne.Epochs.plot() now takes a epochs_colors parameter to color specific epoch segments by Mainak Jas

• Add command mne setup_forward_model to quickly create a BEM model for a subject by Victor Ferat.

• Add command mne prepare_bem_model to quickly create a BEM solution using the linear collocation approach by Victor Ferat.

• Add support for reading .bdip Xfit binary dipole fit files in mne.read_dipole() by Eric Larson

• Allow returning vector source estimates from sparse inverse solvers through pick_ori='vector' by Christian Brodbeck

• Add NIRS support to mne.viz.plot_topomap() and mne.viz.plot_ica_components() by Robert Luke

• Add the ability to mne.channels.equalize_channels() to also re-order the channels and also operate on instances of mne.Info, mne.Forward, mne.Covariance and mne.time_frequency.CrossSpectralDensity by Marijn van Vliet

• Allow mne.channels.read_custom_montage to handle fiducial points for BESA spherical (.elp) files by Richard Höchenberger

• Add rank argument to mne.fit_dipole() by Eric Larson

• Add function to convert events to annotations mne.annotations_from_events() by Nicolas Barascud

• Add function to calculate scalp coupling index for fNIRS data mne.preprocessing.nirs.scalp_coupling_index() by Robert Luke

• Add item argument to mne.Epochs.get_data() for faster access to NumPy data arrays compared to mne.Epochs.__getitem__() for frequent access on large mne.Epochs objects, by Eric Larson

• More accurate coordinate system for Easycap montages in mne.channels.make_standard_montage() by Christian Brodbeck

• Add border argument to mne.viz.plot_topomap(). border controls the value of the edge points to which topomap values are extrapolated. border='mean' sets these points value to the average of their neighbours. By Mikołaj Magnuski

• Add function mne.viz.link_brains() to link time properties of multiple brain objects interactively by Guillaume Favelier

• Add function mne.preprocessing.annotate_movement() to annotate periods with head motion and mne.preprocessing.compute_average_dev_head_t() to re-estimate the device to head transform with average head position during segments with acceptable head movement. by Adonay Nunes

• Make selected channels more distinguishable in mne.Epochs.plot_sensors() when using kind='select' by Mikołaj Magnuski

• Allow retrieval of the number of Infomax ICA iterations via the new return_n_iter keyword argument of mne.preprocessing.infomax() by Richard Höchenberger

• Expose the number of ICA iterations during the fitting procedure via the n_iter_ attribute of mne.preprocessing.ICA by Richard Höchenberger

• mne.grand_average() now produces a warning when only a single dataset was passed, instead of raising an error by Richard Höchenberger

• Add nrows and ncols parameters to mne.viz.plot_evoked_topomap(), which allows to create multiline topomap plots for Evoked. By Federico Raimondo

• Improve repr of mne.Info (empty items are not shown anymore) by Clemens Brunner

Bug

• Fix the reduce_rank parameter in mne.beamformer.make_lcmv() and mne.beamformer.make_dics() to reduce the rank of the leadfield first before then reducing the rank of the denominator of the beamformer formula for the inversion by Britta Westner and Eric Larson.

• Fix bug with mne.beamformer.make_lcmv() with data where rank was incorrectly checked by Eric Larson.

• Allow mne.channels.read_dig_hpts() to accept point categories (eg. EEG) to be specified in upper case by Alex Gramfort.

• Fix a bug in mne.MixedSourceEstimate.plot_surface() that prevented plotting in latest PySurfer by Christian O’Reilly.

• Fix method='eLORETA' in mne.minimum_norm.apply_inverse(), by Eric Larson:

  1. regularization, which was off by roughly a factor of a square root

  2. units, which are now nAm instead of being arbitrary

  3. explained variance and residuals, which were previously unavailable

  4. force_equal in the case of loose orientations, which previously defaulted to True now defaults to False. Reapplying orientation priors at each iteration of the algorithm sufficiently preserves a smooth transition between loose=0. to loose=1. without compromising localization accuracy in testing.

• Fix bug in method='eLORETA' for mne.minimum_norm.apply_inverse() (and variants) to allow restricting source estimation to a label by Luke Bloy

• Fix bug in mne.compute_covariance() and mne.compute_raw_covariance() where biased normalization (based on degrees of freedom) was used and cov.nfree was not set properly by Eric Larson

• Fix mne.VectorSourceEstimate.normal() to account for cortical patch statistics using use_cps=True by Eric Larson

• Fix pick_ori='normal' for mne.minimum_norm.apply_inverse() when the inverse was computed with loose=1. and the forward solution was not in surface orientation, by Eric Larson

• Fix missing xlabel for mne.io.Raw.plot_psd() and similar functions when passing a subset of axes from a figure by Alex Gramfort

• Fix wrong DataFrame index when index=None in methods mne.io.Raw.to_data_frame(), mne.Epochs.to_data_frame(), mne.Evoked.to_data_frame(), and mne.SourceEstimate.to_data_frame(), by Daniel McCloy.

• Fix incorrect scaling of cluster temporal extent in mne.stats.summarize_clusters_stc() by Daniel McCloy.

• Fix mne.time_frequency.read_tfrs() to properly read Info transforms by Eric Larson

• Fix mne.viz.plot_sensors() to always plot in head coordinate frame by Daniel McCloy.

• Fix mne.io.read_raw_cnt() for version 1 of format in the presence of annotations by Alex Gramfort.

• Fix mne.decoding.GeneralizingEstimator and related classes to support multi-class sklearn scorers such as 'roc_auc_ovo' and 'roc_auc_ovo_weighted' by Eric Larson

• Fix mne.io.read_raw_ctf() to set measurement date from CTF ds files by Luke Bloy.

• Fix mne.read_epochs_eeglab() that ignored channel locations by Alex Gramfort.

• Fix mne.io.read_raw_brainvision() when channel names have spaces by Sebastian Major.

• Fix mne.io.read_raw_brainvision() when "Core" is in the data header by Eric Larson

• Fix mne.io.Raw.anonymize() to correctly reset raw.annotations.orig_time by Luke Bloy.

• Fix mne.io.Raw.anonymize() to correctly avoid shifting raw.annotations.onset relative to raw.first_samp by Eric Larson

• Fix mne.io.Raw.set_channel_types() and mne.io.Raw.rename_channels() and related methods to return the instance instead of None by Eric Larson

• mne.Epochs.iter_evoked() now does not return a copy of info when copy=False (default parameter) by Alex Gramfort

• The attribute mne.Annotations.orig_time is now read-only, and is a datetime object (or None) rather than float, by Eric Larson

• Fix bug where MRI distances were not properly initialized in mne coreg by Eric Larson

• Fix xscale='log' in mne.io.Raw.plot_psd() and related functions by Alex Gramfort

• Unify behavior of raw.annotations.append(...) when raw.info['meas_date'] is None to make onsets absolute relative to first_samp as they are when raw.info['meas_date'] is not None; i.e., you might need to do raw.annotations.append(old_time + raw.first_time), by Eric Larson

• The info['meas_date'] entry is now a datetime object (or None) rather than float, by Eric Larson

• Fix mne.time_frequency.AverageTFR.save() and related functions to deal with datetime objects properly by Eric Larson

• Fix date reading before Unix time zero (1970 Jan 1) on Windows by Alex Rockhill.

• Fix bug running subprocesses (e.g., in mne.bem.make_watershed_bem()) in Jupyter notebooks, by Eric Larson

• Fix mne.io.read_raw_artemis123() to add HPI locations to digitization points, by Luke Bloy

• Fix mne.Epochs.shift_time() and mne.Evoked.shift_time() to return the modified Epochs or Evoked instance (instead of None) by Daniel McCloy.

• Fix mne.read_annotations() for text files with zero or one annotations, by Adonay Nunes

• Fix bug in ICA where requesting extended infomax via fit_params={'extended': True} was overridden, by Daniel McCloy.

• Fix bug in mne.Epochs.interpolate_bads() where the origin was not used during MEG or EEG data interpolation by Eric Larson. Old behavior can be achieved using origin=(0., 0., 0.) for EEG and origin=(0., 0., 0.04) for MEG, and the new default is origin='auto', which uses a head-digitization-based fit.

• Fix bug in mne.write_evokeds() where evoked.nave was not saved properly when multiple Evoked instances were written to a single file, by Eric Larson

• Fix bug in mne.preprocessing.mark_flat where acquisition skips were not handled properly, by Eric Larson

• Fix bug in mne.viz.plot_bem() where some sources were not plotted by Jean-Remi King and Eric Larson

• Fix TAL channel parsing (annotations) for EDF-D files by Clemens Brunner

• Fix bug with mne.viz.plot_dipole_locations() when plotting in head coordinates by Eric Larson

• Fix handling in cases where no components are found in mne.preprocessing.corrmap() by Eric Larson

• Fix handling of repeated events in mne.Epochs by Fahimeh Mamashli and Alex Gramfort

• Fix many bugs with plotting sensors overlaid on a head outline. All plotting is now done in head coordinates and scaled by head_radius, which defaults to 0.095, by Eric Larson

• Fix mne.io.anonymize_info() to allow shifting dates of service and to match anticipated changes in mne-cpp by Luke Bloy

• Fix reading of cardinals in .htps files (identifier are int not strings) by Alex Gramfort

• Fix IO of TFRs when event_id contain a / in one of the keys by Alex Gramfort

• Fix plotting of TFRs with linear y-scale (misaligned frequency bins), by Stefan Repplinger and Eric Larson

• Fix info['sfreq'] when decimating in mne.time_frequency.tfr_multitaper() and mne.time_frequency.tfr_morlet() and make sure an error is raised when exceed Nyquist frequency by Adonay Nunes

• Fix bug in EDF(+) loading, filter values ignored by insufficient regex, by Demetres Kostas

• Fix missing scaling of tolerance parameter in mne.inverse_sparse.tf_mixed_norm() and mne.inverse_sparse.mixed_norm(), by Mathurin Massias

• Fix the automatic scaling of the glyphs in mne.viz.plot_vector_source_estimates() by using 10% of the brain width, by Guillaume Favelier

• Fix handling of missing values (NaNs) in mne.time_frequency.psd_welch() by Clemens Brunner

• Fix mne.decoding.LinearModel to support the refitted estimator of GridSearchCV in sklearn by Chun-Hui Li

• Fix mne.viz.plot_topomap() when there are bad channels in the provided mne.Info instance by Eric Larson

• Fix check for subject definition existing in source space in mne.compute_source_morph() and related functions by Eric Larson

• Fix creation of new figures in mne.Epochs.plot_image() and mne.viz.plot_epochs_image() by Eric Larson

• Fix bug in Xdawn where filters where selected along the incorrect axis, by Henrich Kolkhorst

• Fix bug in mne.bem.make_watershed_bem() where some surfaces were saved incorrectly in the working directory by Yu-Han Luo

• Fix support for multiple TAL (annotations) channels in BDF reader by Clemens Brunner

• Fix missing brainmask file type in mne.bem.make_watershed_bem() by changing its default value to ws.mgz by Fu-Te Wong

• Fix bug in mne.channels.make_standard_montage() which would return easycap-M1 even when requesting easycap-M10 by Christian Brodbeck

• Fix the way planar gradiometers are combined in mne.viz.plot_tfr_topomap() and mne.Epochs.plot_psd_topomap() by Geoff Brookshire

• Improve error message when trying to load FieldTrip data from a cell array by Thomas Hartmann

• Fix bug in mne.read_evoked_fieldtrip() causing it to crash when channels were present in the provided Info object but were not present in the data by Thomas Hartmann

• Fix placement of extrapolation points in mne.Evoked.plot_topomap() and related functions when exactly three channels were used by Mikołaj Magnuski.

• Fix bug in reading annotations in read_annotations(), which would not accept “;” character by Adam Li

• Fix bug in mne.Report.parse_folder(), which would not recognize *meg.fif files by Dmitrii Altukhov.

• Include fit_params when saving an ICA instance to disk by Richard Höchenberger

• Update old url link in mne.datasets.eegbci.load_data() to EEGMI_URL = 'https://physionet.org/files/eegmmidb/1.0.0/' by Ramiro Gatti

• Ensure corrected p-values calculated by mne.stats.bonferroni_correction() never exceed the value of 1.0 by Richard Höchenberger

API

• mne.io.pick.get_channel_types is now called mne.io.pick.get_channel_type_constants to better reflect its return values, by Daniel McCloy.

• mne.Evoked.as_type() now returns an instance of mne.EvokedArray by Sophie Herbst and Alex Gramfort

• Bumped minimum requirements to fall 2017 versions by Eric Larson:

  • NumPy 1.13.3

  • SciPy 1.0.0

  • matplotlib 2.1

  • scikit-learn 0.19.1 (optional requirement)

  • pandas 0.21 (optional requirement)

• mne.Epochs.plot() now accepts an event_id parameter (useful in tandem with event_colors for specifying event colors by name) by Daniel McCloy.

• Passing ch_types=None has been deprecated in favor of explicitly passing ch_types='misc' in mne.create_info() by Eric Larson

• New time conversion options for methods mne.io.Raw.to_data_frame(), mne.Epochs.to_data_frame(), mne.Evoked.to_data_frame(), and mne.SourceEstimate.to_data_frame(), by Daniel McCloy.

• mne.Epochs.shift_time() and mne.Evoked.shift_time() now allow shifting times by arbitrary amounts (previously only by integer multiples of the sampling period), by Daniel McCloy and Eric Larson.

• The head_pos argument of mne.Evoked.plot_topomap() and related functions has been deprecated in favor of head_radius, by Eric Larson.

• The layout argument to topomap-related functions such as mne.Evoked.plot_topomap() and mne.viz.plot_tfr_topomap() has been deprecated in favor of channel-position based flattening based on the info and sphere argument, by Eric Larson.

• The APIs of mne.io.Raw.plot_projs_topomap(), mne.Epochs.plot_projs_topomap() and mne.Evoked.plot_projs_topomap() are now more similar to mne.viz.plot_projs_topomap() by Daniel McCloy.

• The function mne.setup_volume_source_space() has a sphere_units argument that defaults to 'mm' in 0.20 but will change to 'm' in 0.21, set it to avoid a warning by Eric Larson.

• mne.viz.plot_projs_topomap() and the related methods mne.io.Raw.plot_projs_topomap(), mne.Epochs.plot_projs_topomap() and mne.Evoked.plot_projs_topomap() now accept parameter vlim to control the colormap, with keyword 'joint' computing the colormap jointly across all projectors of a given channel type, by Daniel McCloy.

• New methods mne.io.Raw.get_channel_types(), mne.Epochs.get_channel_types(), mne.Evoked.get_channel_types() by Daniel McCloy.

• Deprecate mne.minimum_norm.point_spread_function and mne.minimum_norm.cross_talk_function by Alex Gramfort

• Deprecate montage parameter of mne.create_info() in favor of mne.io.Raw.set_montage(), mne.Info.set_montage(), and related functions by Eric Larson

• mne.channels.equalize_channels() no longer operates in-place by default, but instead makes copies of the objects when necessary (see copy parameter) by Marijn van Vliet

• mne.channels.equalize_channels() now uses the first object in the list as a template for channel ordering by Marijn van Vliet

• mne.channels.equalize_channels() now also re-orders the channels to match, in addition to dropping channels that are not shared by all objects by Marijn van Vliet

• mne.io.Raw.pick_channels(), mne.Epochs.pick_channels() and mne.Evoked.pick_channels() now have an ordered parameter to enforce the ordering of the picked channels by Marijn van Vliet

• New methods mne.Forward.pick_channels(), mne.Covariance.pick_channels(), mne.Info.pick_channels(), mne.time_frequency.CrossSpectralDensity.pick_channels() by Marijn van Vliet

• New attributes mne.Forward.ch_names and mne.Info.ch_names by Marijn van Vliet

• In Xdawn, the components are stored in the rows of attributes filters_ and patterns_ to be consistent with CSP and ICA by Henrich Kolkhorst

• Drop unit keyword argument from mne.channels.read_custom_montage(), as it was unused by Richard Höchenberger

• Deprecate mne.preprocessing.run_ica, use mne.preprocessing.ICA.detect_artifacts() instead by Richard Höchenberger

Authors

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

• Adam Li

• Adonay Nunes

• Alex Rockhill

• Alexandre Gramfort

• Ariel Rokem

• Britta Westner

• Carlos de la Torre

• Christian Brodbeck

• Christian O’Reilly

• Chun-Hui Li

• Clemens Brunner

• Daniel McCloy

• Demetres Kostas

• Denis A. Engemann

• Dmitrii Altukhov

• Dominik Welke

• Eric Larson

• Ezequiel Mikulan

• Fahimeh Mamashli

• Fede Raimondo

• Fu-Te Wong

• Geoff Brookshire

• Guillaume Favelier

• Henrich Kolkhorst

• Joan Massich

• José C. García Alanis

• Jussi Nurminen

• Kaisu Lankinen

• Luke Bloy

• Mainak Jas

• Marijn van Vliet

• Mathurin Massias

• Mikolaj Magnuski

• Mohamed Sherif

• Mohammad Daneshzand

• Nataliia Kozhemiako

• Nicolas Barascud

• Nicolas Legrand

• Olaf Hauk

• Padma Sundaram

• Ramiro Gatti

• Richard Höchenberger

• Robert Luke

• Robert Oostenveld

• Sebastian Major

• Sophie Herbst

• Stefan Appelhoff

• Stefan Repplinger

• Thomas Hartmann

• Victor Férat

• Yu-Han Luo

Version 0.19

Changelog

• Add mne.cuda.set_cuda_device() and config variable MNE_CUDA_DEVICE to select among multiple GPUs (by numeric device ID) by Daniel McCloy.

• Add mne.channels.make_standard_montage() to create mne.channels.DigMontage from templates by Joan Massich and Alex Gramfort.

• Add mne.channels.compute_dev_head_t() to compute Device-to-Head transformation from a montage by Joan Massich and Alex Gramfort.

• Add mne.channels.read_dig_fif() to read digitization coordinates from .fif files by Joan Massich and Alex Gramfort.

• Add mne.channels.read_dig_egi() to read digitization coordinates from EGI .xml files by Joan Massich and Alex Gramfort.

• Add mne.channels.read_dig_polhemus_isotrak() and 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 mne.channels.make_dig_montage() to create mne.channels.DigMontage objects out of np.arrays by Joan Massich

• Add 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 mne.Epochs by Stefan Appelhoff

• Allow 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 Theodore Papadopoulo

• Now 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 mne watershed_bem by Eric Larson

• Add support to mne.read_annotations() to read CTF marker files by Joan Massich

• Do not convert effective number of averages (nave attribute of mne.Evoked) to integer except when saving to FIFF file by Daniel McCloy.

• Add automatic fiducial position estimation in mne coreg using MNI Talairach fiducial locations in mne.coreg.get_mni_fiducials() by Jon Houck and Eric Larson

• Add support for 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 mne.io.read_raw_curry() by Dirk Gütlin

• Butterfly channel plots now possible for mne.Epochs.plot_psd() with average=False. Infrastructure for this function now shared with analogous Raw function, found in mne.viz.utils by Jeff 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 mne.what() and mne what by Eric Larson

• Add support for specifying the initial time and/or position and providing a mne.SourceMorph instead of mne.SourceSpaces in mne.viz.plot_volume_source_estimates() by Eric Larson

• Speed up morph map generation in mne.read_morph_map() by ~5-10x by using numba.jit() by Eric Larson

• Speed up mne.setup_volume_source_space(), especially when volume_label is not None by Eric Larson

• Speed up mne coreg interactive and automated (ICP) alignment by using nearest-neighbor calculations in the MRI coordinate frame, by Eric Larson

• Add 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 mne.io.Raw.plot() by Eric Larson

• Add mne.viz.plot_brain_colorbar() to plot a colorbar appropriately matched to a 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 mne.viz.plot_alignment() by Eric Larson

• Add option include_tmax=True to cropping methods mne.io.Raw.crop(), mne.Epochs.crop(), mne.Evoked.crop(), mne.SourceEstimate.crop(), mne.Dipole.crop(), and mne.time_frequency.AverageTFR.crop() by Eric Larson

• Change the behavior of 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 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 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 mne.Info by Eric Larson

• Add control over dipole colors in mne.viz.plot_dipole_locations() when using orthoview mode by Eric Larson

• Use second-order-sections filtering in mne.io.Raw.plot() and mne browse_raw by Eric Larson

• Add re-referencing functionality for ecog and seeg channel types in 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

• 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 mne.grand_average() to use equal sum-to-one weights (like it used to, before changes to underlying mne.combine_evoked()) by Daniel McCloy

• Fix mne.io.Raw.filter() to deal with instances with no data channels properly by Eric Larson

• Fix one-sample baseline issue in mne.BaseEpochs when using tmin=0 by Milan Rybář

• Fix bug in mne.viz.plot_volume_source_estimates() where 'glass_brain' MRIs were not transformed to MNI space, by Eric Larson

• Fix bug in 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 mne.SourceMorph.apply() where output STCs had stc.vertices defined improperly, by Eric Larson

• Fix bug in 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 mne.minimum_norm.apply_inverse() to only allow normal extraction/orientation for surface and discrete source spaces by Eric Larson

• Fix mne.io.Raw.set_annotations() for meas_date previous to 1970 by Joan Massich

• Fix horizontal spacing issues in mne.io.Raw.plot_psd() by Jeff 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 mne.io.Raw.plot_psd() by Eric Larson

• Fix side-effect where mne.viz.plot_ica_sources() and 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 ica.plot_sources(epochs) 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 mne.io.read_raw_edf() by Alex Gramfort

• Fix 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 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 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 mne.io.read_raw_bti() by Joshua Bear and Eberhard Eich

• Fix formula for effective number of averages in mne.combine_evoked() when weights='equal' by Daniel McCloy.

• Fix bug in 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 mne.events_from_annotations() to recover Brainvision markers after saving it in .fif by Joan Massich

• Fix mne.read_epochs_eeglab() when epochs are stored as float. By Thomas Radman

• Fix mne.Evoked.resample() and mne.Epochs.resample() not setting inst.info['lowpass'] properly by Eric Larson

• Fix checks when constructing volumetric and surface source spaces with mne.setup_volume_source_space() and mne.setup_source_space(), respectively, by Eric Larson

• Fix bug in handling of mne.Evoked types that were not produced by MNE-Python (e.g., alternating average) by Eric Larson

• Fix bug in mne.read_source_estimate() where vector volumetric source estimates could not be read by Eric Larson

• Fix bug in mne.inverse_sparse.mixed_norm() and mne.inverse_sparse.tf_mixed_norm() where weights was supplied but weights_min was not, by Eric Larson

• Fix bug in 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 mne.io.Raw.plot() when using HiDPI displays and the MacOSX backend of matplotlib by Eric Larson

• Fix bug in mne.viz.plot_compare_evokeds() when using Neuromag 122 system by Eric Larson

• Fix bug in mne.Epochs.plot_psd() when some channels had zero/infinite psd values causing erroneous error messages by Luke Bloy

• Fix mne.Evoked.decimate() not setting inst.first and inst.last properly by Marijn van Vliet

• Fix mne.io.read_raw_brainvision() not handling Event markers created by PyCorder correctly by Richard Höchenberger

• Fix support for string-like objects (such as pathlib.Path) by Eric Larson

• Fix 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 mne.io.Raw.set_montage() by Joan Massich.

• Deprecate set_dig parameter in mne.io.Raw.set_montage() and update_ch_names in mne.io.RawEEGLAB.set_montage when using mne.channels.DigMontage as by Joan Massich.

• Now mne.io.Raw.set_montage() raises an error when 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 mne.io.Raw.plot(), mne.Epochs.plot(), and 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 mne.grand_average() (which works on both Evoked and AverageTFR) by Daniel McCloy

• Deprecate exclude parameter in mne.viz.plot_ica_sources() and 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 mne.io.read_raw_cnt(), mne.io.read_raw_egi(), mne.io.read_raw_edf(), mne.io.read_raw_gdf(), mne.io.read_raw_nicolet(), mne.io.read_raw_eeglab() and mne.read_epochs_eeglab() by Alex Gramfort

• New parameter clear in mne.viz.plot_epochs_image() for clearing pre-existing axes before plotting into them by Daniel McCloy

• 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 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 mne.viz.plot_compare_evokeds() is deprecated; use combine='gfp' instead by Daniel McCloy

• The truncate_yaxis='max_ticks' parameter of mne.viz.plot_compare_evokeds() is deprecated; use truncate_yaxis='auto' instead by Daniel McCloy

• The truncate_xaxis and truncate_yaxis parameters of mne.viz.plot_compare_evokeds() now perform one-sided truncation unless both are True by Daniel McCloy

• The show_legend parameter of mne.viz.plot_compare_evokeds() is renamed to legend by Daniel McCloy

• 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 mne.Epochs.plot_psd() by Jeff Hanna

• 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 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

Version 0.18

Changelog

• Add event_id='auto' in mne.events_from_annotations() to accommodate Brainvision markers by Jona Sassenhagen, Joan Massich and Eric Larson

• Add example on how to simulate raw data using subject anatomy, by Ivana Kojcic,`Eric Larson`_,`Samuel Deslauriers-Gauthier`_ and`Kostiantyn Maksymenko`_

• mne.beamformer.apply_lcmv_cov() returns static source power after supplying a data covariance matrix to the beamformer filter by Britta Westner and Marijn van Vliet

• Add butterfly and order arguments to mne.viz.plot_epochs() and offer separated traces for non-meg data (seeg, eeg, ecog) in butterfly view by Stefan Repplinger and Eric Larson

• mne.Epochs.get_data() now takes a picks parameter by Jona Sassenhagen

• plot_compare_evokeds() will generate topo plots if axes='topo' by Jona Sassenhagen

• mne.viz.iter_topography can yield an additional axis, e.g., for plotting legends by Jona Sassenhagen and Daniel McCloy

• Default plot title reflects channel type when picks is a channel type in plot_compare_evokeds() by Daniel McCloy

• Color scale limits in plot_topo_image_epochs() are now computed separately per channel type in combined mag/grad plots, by Daniel McCloy

• mne.simulation.simulate_stc() now allows for label overlaps by Nathalie Gayraud, and Ivana Kojcic

• Add long_format option to the pandas dataframe exporters, e.g mne.Epochs.to_data_frame() by Denis Engemann

• Add example on how to load standard montage Plotting sensor layouts of EEG systems by Joan Massich

• Add new tutorial on EEG forward operator with a template MRI by Alex Gramfort, and Joan Massich

• Add mne.Epochs.apply_hilbert() and mne.Evoked.apply_hilbert() by Eric Larson

• Add convenience fsaverage subject dataset fetcher / updater mne.datasets.fetch_fsaverage() by Eric Larson

• Add fmin and fmax argument to mne.time_frequency.AverageTFR.crop() and to mne.time_frequency.EpochsTFR.crop() to crop TFR objects along frequency axis by Dirk Gütlin

• Add support to mne.read_annotations() to read CNT formats by Joan Massich

• Add reject parameter to mne.preprocessing.ICA.plot_properties() to visualize rejected epochs by Antoine Gauthier

• Add support for picking channels using channel name and type strings to functions with picks arguments, along with a convenience mne.io.Raw.pick(), mne.Epochs.pick(), and mne.Evoked.pick() method, by Eric Larson

• Add new tutorial on Sleep stage classification from polysomnography (PSG) data by Alex Gramfort, Stanislas Chambon and Joan Massich

• Add data fetchers for polysomnography (PSG) recordings from Physionet (mne.datasets.sleep_physionet.age.fetch_data() and mne.datasets.sleep_physionet.temazepam.fetch_data()) by Alex Gramfort and Joan Massich

• Add envelope correlation code in mne.connectivity.envelope_correlation() by Denis Engemann, Sheraz Khan, and Eric Larson

• Add option to toggle all projectors in mne.io.Raw.plot() and related functions by Eric Larson

• Add support for indexing, slicing, and iterating mne.Annotations by Joan Massich

• mne.io.Raw.plot() now uses the lesser of n_channels and raw.ch_names, by Joan Massich

• Add support for FIR filtering in mne.io.Raw.plot() and mne browse_raw by passing filtorder=0 or --filtorder 0, respectively, by Eric Larson

• Add chunk_duration parameter to mne.events_from_annotations() to allow multiple events from a single annotation by Joan Massich

• Add mne.simulation.SourceSimulator class to simplify simulating SourceEstimates, by Samuel Deslauriers-Gauthier, Kostiantyn Maksymenko, Nathalie Gayraud, Ivana Kojcic, Alex Gramfort, and Eric Larson

• mne.io.read_raw_edf() now detects analog stim channels labeled 'STATUS' and sets them as stim channel. mne.io.read_raw_edf() no longer synthesize TAL annotations into stim channel but stores them in raw.annotations when reading by Joan Massich

• Add mne.simulation.add_noise for ad-hoc noise addition to io.Raw, Epochs, and Evoked instances, by Eric Larson

• Add drop_refs=True parameter to set_bipolar_reference() to drop/keep anode and cathode channels after applying the reference by Cristóbal Moënne-Loccoz.

• Add processing of reference MEG channels to mne.preprocessing.ICA by Jeff Hanna

• Add use of scipy.signal.windows.dpss() for faster multitaper window computations in PSD functions by Eric Larson

• Add mne.morph_labels() to facilitate morphing label sets obtained from parcellations, by Eric Larson

• Add mne.labels_to_stc() to facilitate working with label data, by Eric Larson

• Add mne.label.select_sources() to simplify the selection of sources within a label, by Samuel Deslauriers-Gauthier

• Add support for using mne.Info in mne.simulation.simulate_raw() instead of mne.io.Raw by Eric Larson

• Add support for passing an iterable and stim channel values using stc parameter of mne.simulation.simulate_raw() by Eric Larson

• Add overlap argument to mne.make_fixed_length_events() by Eric Larson

• Add approximate distance-based spacing source space decimation algorithm to mne.setup_source_space() by Eric Larson

• Add 448-labels subdivided aparc cortical parcellation by Denis Engemann and Sheraz Khan

• Add option to improve rendering in mne coreg for modern graphics cards by Eric Larson

• Add mne.preprocessing.mark_flat to automate marking of flat channels and segments of raw data by Eric Larson

• Add support for CUDA-based correlation computations and progress bars in mne.decoding.ReceptiveField by Eric Larson

• Add support for file-like objects in mne.io.read_raw_fif() as long as preloading is used by Eric Larson

• Add keyboard shortcuts to nativate volume source estimates in time using (shift+)left/right arrow keys by Mainak Jas

• Add option to SSP preprocessing functions (e.g., mne.preprocessing.compute_proj_eog() and mne.compute_proj_epochs()) to process MEG channels jointly with meg='combined' by Eric Larson

• Add Epoch selection and metadata functionality to mne.time_frequency.EpochsTFR using new mixin class by Keith Doelling

• Add reject_by_annotation argument to mne.preprocessing.find_ecg_events() by Eric Larson

• Add pca argument to return the rank-reduced whitener in mne.cov.compute_whitener() by Eric Larson

• Add extrapolate argument to mne.viz.plot_topomap() for better control of extrapolation points placement by Mikołaj Magnuski

• Add channel_wise argument to mne.io.Raw.apply_function() to allow applying a function on multiple channels at once by Hubert Banville

• Add option copy='auto' to control data copying in mne.io.RawArray by Eric Larson

• The mri parameter in mne.setup_volume_source_space() is now automatically set to T1.mgz if subject is provided. This allows to get a mne.SourceSpaces of kind volume more automatically. By Alex Gramfort

• Add better __repr__ for constants, and info['dig'] entries via DigPoint by Eric Larson

• Allow string argument in mne.io.Raw.drop_channels() to remove a single channel by Clemens Brunner

• Add additional depth weighting options for inverse solvers (e.g., mne.inverse_sparse.gamma_map() and mne.inverse_sparse.mixed_norm()) by Eric Larson

• Add depth weighting to LCMV beamformers via depth argument in mne.beamformer.make_lcmv() by Eric Larson

• Allow toggling of DC removal in mne.io.Raw.plot() by pressing the ‘d’ key by Clemens Brunner

• Improved clicking in mne.io.Raw.plot() (left click on trace toggles bad, left click on background sets green line, right click anywhere removes green line) by Clemens Brunner

• Add mne.realtime.LSLClient for realtime data acquisition with LSL streams of data by Teon Brooks and Mainak Jas

• Add partial support for PyVista as a 3D backend using mne.viz.use_3d_backend() by Guillaume Favelier

• Add option ids = None in mne.event.shift_time_events() for considering all events by Nikolas Chalas and Joan Massich

• Add mne.realtime.MockLSLStream to simulate an LSL stream for testing and examples by Teon Brooks

• Add support for file-like objects in mne.read_epochs() as long as preloading is used by Paul Roujansky

Bug

• Fix annotations in split fif files mne.io.read_raw_fif() by Joan Massich

• Fix mne.Epochs.plot() with scalings='auto' to properly compute channel-wise scalings by Stefan Repplinger

• Fix mne.gui.coregistration() and mne coreg crashing with segmentation fault when switching subjects by Eric Larson

• Fix mne.io.read_raw_brainvision() to accommodate vmrk files which do not have any annotations by Alexander Kovrig

• Fix mne.io.Raw.plot() and mne.Epochs.plot() to auto-scale misc channel types by default by Eric Larson

• Fix filtering functions (e.g., mne.io.Raw.filter()) to properly take into account the two elements in n_pad parameter by Bruno Nicenboim

• Fix feature_names parameter change after fitting in mne.decoding.ReceptiveField by Jean-Remi King

• Fix index error in mne.io.read_raw_cnt() when creating stim_channel manually by Joan Massich

• Fix bug with weight_norm='unit-gain' in mne.beamformer.make_lcmv() and mne.beamformer.make_dics() by Britta Westner

• Fix 32bits annotations in mne.io.read_raw_cnt() by Joan Massich

• Fix mne.events_from_annotations() to ignore 'BAD_'` and ``'EDGE_' annotations by default using a new default regexp by Eric Larson

• Fix bug in mne.preprocessing.mark_flat where raw.first_samp was not taken into account by kalenkovich

• Fix date parsing in mne.io.read_raw_cnt() by Joan Massich

• Fix topological checks and error messages for BEM surfaces in mne.make_bem_model() by Eric Larson

• Fix default HTML language of mne.Report to be "en-us" instead of "fr" and allow setting via report.lang property by Eric Larson

• Fix bug where loading epochs with preload=True and subsequently using mne.Epochs.drop_bad() with new reject or flat entries leads to improper data (and epochs.selection) since v0.16.0 by Eric Larson. If your code uses Epochs(..., preload=True).drop_bad(reject=..., flat=...), we recommend regenerating these data.

• Fix mne flash_bem to properly utilize flash30 images when conversion from DICOM images is used, and to properly deal with non-standard acquisition affines by Eric Larson

• Fix mne.io.Raw.set_annotations() with annotations=None to create an empty annotations object with orig_time that matches the mne.io.Raw instance by Eric Larson

• Fix mne.io.read_raw_edf() returning all the annotations with the same name in GDF files by Joan Massich

• Fix boundaries during plotting of raw data with mne.io.Raw.plot() and mne browse_raw on scaled displays (e.g., macOS with HiDPI/Retina screens) by Clemens Brunner

• Fix bug where filtering was not performed with lowpass or highpass in mne.io.Raw.plot() and mne browse_raw by Eric Larson

• Fix mne.simulation.simulate_evoked() that was failing to simulate the noise with heterogeneous sensor types due to poor conditioning of the noise covariance and make sure the projections from the noise covariance are taken into account Alex Gramfort

• Fix checking of data dimensionality in mne.SourceEstimate and related constructors by Eric Larson

• Fix mne.io.Raw.append() annotations miss-alignment by Joan Massich

• Fix hash bug in the mne.io.edf module when installing on Windows by Eric Larson

• Fix mne.io.read_raw_edf() reading duplicate channel names by Larry Eisenman

• Fix set_bipolar_reference() in the case of generating all bipolar combinations and also in the case of repeated channels in both lists (anode and cathode) by Cristóbal Moënne-Loccoz

• Fix missing code for computing the median when method='median' in mne.Epochs.average() by Cristóbal Moënne-Loccoz

• Fix CTF helmet plotting in mne.viz.plot_evoked_field() by Eric Larson

• Fix saving of rejection parameters in mne.Epochs.save() by Eric Larson

• Fix orientations returned by mne.dipole.get_phantom_dipoles() (half were flipped 180 degrees) by Eric Larson

• Fix bug in mne.viz.plot_compare_evokeds() when evoked.times[0] >= 0 would cause a problem with vlines='auto' mode by Eric Larson

• Fix path bugs in mne.bem.make_flash_bem() and mne flash_bem by Eric Larson

• Fix mne.time_frequency.AverageTFR.plot_joint() mishandling bad channels, by David Haslacher and Jona Sassenhagen

• Fix mne.beamformer.make_lcmv() failing when full rank data is used (i.e., when no projection is done) with reg=0., by Eric Larson

• Fix issue with bad channels ignored in mne.beamformer.make_lcmv() and mne.beamformer.make_dics() by Alex Gramfort

• Fix mne.compute_proj_raw() when duration != None not to apply existing proj and to avoid using duplicate raw data samples by Eric Larson

• Fix reject_by_annotation not being passed internally by mne.preprocessing.create_ecg_epochs() and mne clean_eog_ecg to mne.preprocessing.find_ecg_events() by Eric Larson

• Fix mne.io.read_raw_edf() failing when EDF header fields (such as patient name) contained special characters, by Clemens Brunner

• Fix mne.io.read_raw_eeglab() incorrectly parsing event durations by Clemens Brunner

• Fix mne.io.read_raw_egi() when cropping non-preloaded EGI MFF data by Alex Gramfort

• Fix mne.io.Raw.interpolate_bads() for interpolating CTF MEG channels when reference sensors are present by jeythekey

• Fix a bug in mne.io.Raw.resample(), where resampling events could result in indices > n_times-1, by jeythekey

• Fix mne.preprocessing.ICA.score_sources() to use the sfreq of the raw data to filter rather than the sfreq when the ICA was fit, by jeythekey

• Fix a bug in mne.preprocessing.ICA, where manually setting the attribute ICA.exclude to an np.array resulted in the removal of random components when later also providing the exclude argument to any apply...-method, by jeythekey

• Ascending changed to descending sorting of scores for integer ..._criterion arguments in mne.preprocessing.ICA.detect_artifacts() and mne.preprocessing.run_ica, as it used to be documented; the docstring in these functions was corrected for float ..._criterion arguments, by jeythekey

API

• Deprecate cov, iir_params, blink, ecg, chpi, random_state and support for mne.io.Raw instance inputs in mne.simulation.simulate_raw(); use mne.simulation.add_noise(), mne.simulation.add_ecg(), mne.simulation.add_eog(), and mne.simulation.add_chpi() by Eric Larson

• Add overwrite parameter in mne.Epochs.save() by Katarina Slama

• Add stim_channel parameter in mne.io.read_raw_cnt() to toggle stim channel synthesis by Joan Massich

• Python 2 is no longer supported; MNE-Python now requires Python 3.5+, by Eric Larson

• A new class mne.VolVectorSourceEstimate is returned by mne.minimum_norm.apply_inverse() (and related functions) when a volume source space and pick_ori='vector' is used, by Eric Larson

• Converting a forward solution with a volume source space to fixed orientation using mne.convert_forward_solution() now raises an error, by Eric Larson

• raw.estimate_rank has been deprecated and will be removed in 0.19 in favor of mne.compute_rank() by Eric Larson

• Annotations are now kept sorted (by onset time) during instantiation and append() operations, by Eric Larson

• Deprecate mne.io.find_edf_events by Joan Massich

• Deprecate limit_depth_chs in mne.minimum_norm.make_inverse_operator() in favor of depth=dict(limit_depth_chs=...) by Eric Larson

• Reading BDF and GDF files with mne.io.read_raw_edf() is deprecated and replaced by mne.io.read_raw_bdf() and mne.io.read_raw_gdf(), by Clemens Brunner

• mne.forward.compute_depth_prior() has been reworked to operate directly on Forward instance as forward rather than a representation scattered across the parameters G, is_fixed_ori, patch_info, by Eric Larson

• Deprecate method='extended-infomax' in mne.preprocessing.ICA; Extended Infomax can now be computed with method='infomax' and fit_params=dict(extended=True) by Clemens Brunner

• Fix support for supplying extrapolate via ica.plot_properties(..., topomap_args=dict(extrapolate=...)) by Sebastian Castano

• The peak finder that was formerly accessible via from mne.preprocessing.peak_finder import peak_finder should now be imported directly from the enclosing namespace as from mne.preprocessing import peak_finder by Eric Larson

• Deprecate mne.realtime module to make a standalone module mne-realtime that will live outside of this package by Teon Brooks

Version 0.17

Changelog

• Add new tutorial for mne.Annotations and events by Joan Massich and Alex Gramfort

• Add support for saving mne.Annotations as CSV and TXT files by Joan Massich and Alex Gramfort

• Add mne.Epochs.shift_time() that shifts the time axis of mne.Epochs by Thomas Hartmann

• Add mne.viz.plot_arrowmap() computes arrowmaps using Hosaka-Cohen transformation from magnetometer or gradiometer data, these arrows represents an estimation of the current flow underneath the MEG sensors by Sheraz Khan

• Add mne.io.read_raw_fieldtrip(), mne.read_epochs_fieldtrip() and mne.read_evoked_fieldtrip() to import FieldTrip data. By Thomas Hartmann and Dirk Gütlin.

• Add rank parameter to mne.compute_covariance(), mne.cov.regularize() and related functions to preserve data rank and speed up computation using low-rank computations during regularization by Eric Larson and Denis Engemann

• Add new function mne.read_annotations() that can read annotations in EEGLAB, BrainVision, EDF and Brainstorm formats by Joan Massich and Alex Gramfort.

• Add capability to read and save Epochs containing complex data (e.g. after Hilbert-transform) using mne.Epochs.save() and mne.read_epochs(), by Stefan Repplinger, Eric Larson and Alex Gramfort

• Add optically pumped magnetometer dataset and example by Rasmus Zetter and Eric Larson

• Add orgin parameter to mne.io.Raw.time_as_index() to allow times to be relative to this origin by Joan Massich

• Add title argument to mne.SourceEstimate.plot() by Eric Larson

• mne.io.Raw.set_annotations() now changes orig_time to match meas_date and shift self.annotations.onset accordingly. Previous behavior is deprecated and would be removed in 0.18. Work by Joan Massich

• Add mne.compute_source_morph() which creates a mne.SourceMorph object to unify morphing any type of source estimates (surface or volume) from one subject to another for group studies. It is now possible to do group studies when working on the volume with MNE. Work by Tommy Clausner during GSOC 2018 with the help of Alex Gramfort and Eric Larson.

• Add ability to pass threshold for EOG to mne.preprocessing.find_eog_events() and mne.preprocessing.create_eog_epochs() by Peter Molfese

• Add possibility to save mne.VolSourceEstimate and mne.MixedSourceEstimate to HDF5 format (file extension .h5) with mne.VolSourceEstimate.save() and mne.MixedSourceEstimate.save() by Alex Gramfort

• Add replace parameter to mne.io.Raw.add_events() to allow adding events while removing the old ones on the stim channel by Alex Gramfort

• Add ability to pass axes to ts_args and topomap_args of mne.viz.plot_evoked_joint() by Jona Sassenhagen

• Add ability to pass a precomputed forward solution to mne.simulation.simulate_raw() by Eric Larson

• Add ability to read and write beamformers with mne.beamformer.read_beamformer() and mne.beamformer.Beamformer.save by Eric Larson

• Add resting-state source power spectral estimation example sphx_glr_auto_examples_datasets_plot_opm_rest_data.py by Eric Larson, Denis Engemann, and Luke Bloy

• Add mne.channels.make_1020_channel_selections() to group 10/20-named EEG channels by location, by Jona Sassenhagen

• Add helmet for Artemis123 for mne.viz.plot_alignment() by Eric Larson

• Add support for reading MATLAB v7.3+ files in mne.io.read_raw_eeglab() and mne.read_epochs_eeglab() via pymatreader by Steven Gutstein, Eric Larson, and Thomas Hartmann

• Add support for raw PSD plots in mne.Report.parse_folder() via raw_psd argument of mne.Report by Eric Larson

• Add trig_shift_by_type parameter in mne.io.read_raw_brainvision() to allow to specify offsets for arbitrary marker types by Henrich Kolkhorst

• Add progress bar support to mne.decoding.SlidingEstimator and mne.decoding.GeneralizingEstimator by Eric Larson

• Add interactive visualization of volume source estimates using mne.viz.plot_volume_source_estimates() by Mainak Jas

• Add mne.head_to_mri() to convert positions from head coordinates to MRI RAS coordinates, by Joan Massich and Alex Gramfort

• Add improved CTF helmet for mne.viz.plot_alignment() by Eric Larson

• Add handling in mne.combine_evoked() and mne.grand_average() for input with the same channels in different orders, if required, by Jona Sassenhagen

• Add split_naming parameter to the mne.io.Raw.save method to allow for BIDS-compatible raw file name construction by Teon Brooks

• Add origin parameter to mne.Evoked.interpolate_bads() and related methods by Eric Larson

• Add automated MEG helmet shape approximation to mne.viz.plot_alignment() by Eric Larson

• Add capability to save a mne.Report to an HDF5 file to mne.Report.save() by Marijn van Vliet

• Add mne.open_report() to read back a mne.Report object that was saved to an HDF5 file by Marijn van Vliet

• Add multi-taper estimation to mne.minimum_norm.compute_source_psd() by Eric Larson

• Add support for custom, e.g. robust, averaging methods in mne.Epochs.average() by Jona Sassenhagen

• Add support for Neuromag 122 system by Alex Gramfort

• Add function mne.io.read_annotations_brainvision for reading directly Brainvision marker files by Alex Gramfort

• Add mne.Report.remove() method to remove existing figures from a report, by Marijn van Vliet

• Add sign to output of max-power orientation for mne.beamformer.make_dics() by Eric Larson

• Add support for pick_ori='max-power' when weight_norm=None in mne.beamformer.make_lcmv() by Marijn van Vliet

• Add support for weight_norm='nai' for all pick_ori options in mne.beamformer.make_lcmv() by Marijn van Vliet

• Add support for weight_norm='nai' to mne.beamformer.make_dics() by Marijn van Vliet

• Add parameter rank=None to mne.beamformer.make_dics() by Marijn van Vliet

• Add parameter rank='full' to mne.beamformer.make_lcmv(), which can be set to None to auto-compute the rank of the covariance matrix before regularization by Marijn van Vliet

• Handle different time vectors in topography plots using mne.viz.plot_evoked_topo() by Jussi Nurminen

• Speed up mne.inverse_sparse.mixed_norm() if the solver parameter is set to bcd using scipy.linalg.get_blas_funcs() by Quentin Bertrand

Bug

• Fix bug with scaling of data in mne.cov._compute_covariance_auto that was affecting the mne.decoding.SPoC estimator by David Sabbagh

• Fix mne.io.Raw.plot_projs_topomap() by Joan Massich

• Fix bug in mne.minimum_norm.compute_source_psd() where the stc.times output was scaled by 1000, by Eric Larson

• Fix default values for 'diagonal_fixed' estimation method of mne.compute_covariance() to be 0.1 for all channel types, as in mne.cov.regularize() by Eric Larson

• Fix reading edf file annotations by Joan Massich

• Fix bug with reading events from BrainVision files by Stefan Appelhoff

• Fix bug where mne.io.read_raw_eeglab() would warn when the stim channel is populated with an array of zeros by Joan Massich

• Fix 2nd column of events in BrainVision to no longer store duration but rather be contained by raw.annotations by Alex Gramfort

• Fix checking of the correctness of the prepared=True argument in mne.minimum_norm.apply_inverse() and related functions by Eric Larson

• Fix bug of not showing ERD’s in baseline rescaled tfr topomaps if grads are combined by Erkka Heinila

• Fix bug with FIF I/O where strings were written in UTF-8 format instead of Latin-1 by Eric Larson

• Fix bug with reading measurement dates from BrainVision files by Stefan Appelhoff

• Fix bug with mne.fit_dipole where the residual was returned as ndarray instead of mne.Evoked instance, by Eric Larson

• Fix bug with mne flash_bem when flash30 is not used by Eric Larson

• Fix bug with mne.stats.permutation_cluster_test() and mne.stats.spatio_temporal_cluster_test() where threshold=None was not calculated properly for a f-oneway test by Daniel McCloy and Eric Larson

• Fix bug with channel names in mgh70 montage in mne.channels.read_montage by Eric Larson

• Fix duplication of info['hpi_meas'] and info['hpi_results'] by Sara Sommariva

• Fix bug in mne.io.read_raw_edf() when reading large files on Windows by Marcin Koculak

• Fix check in mne.viz.plot_sensors() for invalid channel locations by Eric Larson

• Fix bug in mne.io.read_raw_edf() where GDF files had info['highpass'] and info['lowpass'] set to NaN and info['meas_date'] set incorrectly, by Eric Larson

• Fix bug in mne.preprocessing.ICA.apply() to handle arrays as exclude property by Joan Massich

• Fix bug in method='eLORETA' for mne.minimum_norm.apply_inverse() when using a sphere model and saved inv by Eric Larson

• Fix bug in mne.io.Raw where warnings were emitted when objects were deleted by Eric Larson

• Fix vector data support for mne.VolSourceEstimate by Christian Brodbeck

• Fix bug with IIR filtering axis in mne.filter.filter_data() by Eric Larson

• Fix bug with non-boxcar windows in mne.io.Raw.resample() and mne.filter.resample() by Eric Larson

• Fix bug in mne.minimum_norm.apply_inverse() where applying an MEG-only inverse would raise an error about needing an average EEG reference by Eric Larson

• Fix bug in inst.apply_proj() where an average EEG reference was always added by Eric Larson

• Fix bug in mne.time_frequency.tfr_morlet(), mne.time_frequency.tfr_multitaper(), and mne.time_frequency.tfr_stockwell() where not all data channels were picked by Eric Larson

• Fix bug in mne.preprocessing.ICA.plot_overlay() and mne.make_field_map() for CTF data with compensation by Eric Larson

• Fix bug in mne.create_info() passing int as ch_names on Windows by Eric Larson

• Fix bug in mne.realtime.RtEpochs where events during the buildup of the buffer were not correctly processed when incoming data buffers are smaller than the epochs by Henrich Kolkhorst

• Fix bug in mne.io.read_raw_brainvision() where 1-indexed BrainVision events were not being converted into 0-indexed mne events by Steven Bethard

• Fix bug in mne.viz.plot_snr_estimate() and mne.minimum_norm.estimate_snr() where the inverse rank was not properly utilized (especially affecting SSS’ed MEG data) by Eric Larson

• Fix error when saving stc as nifti image when using volume source space formed by more than one label by Alex Gramfort

• Fix error when interpolating MEG channels with compensation using reference channels (like for CTF data) by Alex Gramfort

• Fix bug in mne.make_sphere_model() where EEG sphere model coefficients were not optimized properly by Eric Larson

• Fix bug in mne.io.read_raw_ctf() to read bad channels and segments from CTF ds files by Luke Bloy

• Fix problem with mne.io.Raw.add_channels() where raw.info['bads'] was replicated by Eric Larson

• Fix bug with mne.Epochs where an error was thrown when resizing data (e.g., during mne.Epochs.drop_bad()) by Eric Larson

• Fix naming of raw.info['buffer_size_sec'] to be raw.buffer_size_sec as it is a writing parameter rather than a measurement parameter by Eric Larson

• Fix EGI-MFF parser not to require dateutil package by Eric Larson

• Fix error when running LCMV on MEG channels with compensation using reference channels (like for CTF data) by Alex Gramfort

• Fix the use of sklearn.model_selection.cross_val_predict() with mne.decoding.SlidingEstimator by Alex Gramfort

• Fix event sample number increase when combining many Epochs objects with mne.concatenate_epochs() with by Jasper van den Bosch

• Fix title of custom slider images to mne.Report by Marijn van Vliet

• Fix missing initialization of self._current in mne.Epochs by Henrich Kolkhorst

• Fix processing of data with bad segments and acquisition skips with new skip_by_annotation parameter in mne.preprocessing.maxwell_filter() by Eric Larson

• Fix symlinking to use relative paths in mne flash_bem` and ``mne watershed_bem by Eric Larson

• Fix error in mne coreg when saving with scaled MRI if fiducials haven’t been saved by Ezequiel Mikulan

• Fix normalization error in mne.beamformer.make_lcmv() when pick_ori='normal', weight_norm='unit_noise_gain' by Marijn van Vliet

• Fix MNE-C installation instructions by buildqa

• Fix computation of max-power orientation in mne.beamformer.make_dics() when pick_ori='max-power', weight_norm='unit_noise_gain' by Marijn van Vliet

API

• Deprecated separate reading of annotations and synthesis of STI014 channels in readers by Joan Massich:

  • Deprecated mne.io.read_annotations_eeglab

  • Deprecated annot and annotmap parameters in read_raw_edf()

  • Deprecated stim_channel parameters in read_raw_edf(), read_raw_brainvision(), and read_raw_eeglab()

  Annotations are now added to raw instances directly upon reading as raw.annotations. They can also be read separately with mne.read_annotations() for EEGLAB, BrainVision, EDF, and Brainstorm formats. Use mne.events_from_annotations(raw.annotations) to convert these to events instead of the old way (using STI014 channel synthesis followed by mne.find_events(raw)).

  In 0.17 (this release)

  Use read_raw_...(stim_channel=False) to disable warnings (and stim channel synthesis), but other arguments for stim_channel will still be supported.

  In 0.18

  The only supported option will be read_raw_...(stim_channel=False), and all stim-channel-synthesis arguments will be removed. At this point, stim_channel should be removed from scripts for future compatibility, but stim_channel=False will still be acceptable for backward compatibility.

  In 0.19

  The stim_channel keyword arguments will be removed from read_raw_... functions.

• Calling :meth:mne.io.pick.pick_info removing channels that are needed by compensation matrices (info['comps']) no longer raises RuntimeException but instead logs an info level message. By Luke Bloy

• mne.Epochs.save() now has the parameter fmt to specify the desired format (precision) saving epoched data, by Stefan Repplinger, Eric Larson and Alex Gramfort

• Deprecated mne.SourceEstimate.morph_precomputed, mne.SourceEstimate.morph, mne.compute_morph_matrix, mne.morph_data_precomputed and mne.morph_data in favor of mne.compute_source_morph(), by Tommy Clausner

• Prepare transition to Python 3. This release will be the last release compatible with Python 2. The next version will be Python 3 only.

• CUDA support now relies on CuPy instead of PyCUDA and scikits-cuda. It can be installed using conda install cupy. By Eric Larson

• Functions requiring a color cycle will now default to Matplotlib rcParams colors, by Stefan Appelhoff

• mne.Evoked.plot_image() has gained the ability to show_names, and if a selection is provided to group_by, axes can now receive a dict, by Jona Sassenhagen

• Calling mne.Epochs.decimate() with decim=1 no longer copies the data by Henrich Kolkhorst

• Removed blocking (waiting for new epochs) in mne.realtime.RtEpochs.get_data() by Henrich Kolkhorst

• Warning messages are now only emitted as warnings.warn_explicit() rather than also being emitted as logging messages (unless a logging file is being used) to avoid duplicate warning messages, by Eric Larson

• Deprecated save_stc_as_volume function in favor of mne.VolSourceEstimate.as_volume() and mne.VolSourceEstimate.save_as_volume() by Alex Gramfort

• src.kind now equals to 'mixed' (and not 'combined') for a mixed source space (made of surfaces and volume grids) by Alex Gramfort

• Deprecation of mne.io.Raw.annotations property in favor of mne.io.Raw.set_annotations() by Joan Massich

• The default value of stop_receive_thread in mne.realtime.RtEpochs.stop has been changed to True by Henrich Kolkhorst

• Using the mne.io.Raw.add_channels() on an instance with memmapped data will now resize the memmap file to append the new channels on Windows and Linux, by Eric Larson

• mne.io.Raw.annotations when missing is set to an empty mne.Annotations rather than None by Joan Massich and Alex Gramfort

• Mismatches in CTF compensation grade are now checked in inverse computation by Eric Larson

Authors

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

• Alexandre Gramfort

• Antoine Gauthier

• Britta Westner

• Christian Brodbeck

• Clemens Brunner

• Daniel McCloy

• David Sabbagh

• Denis A. Engemann

• Eric Larson

• Ezequiel Mikulan

• Henrich Kolkhorst

• Hubert Banville

• Jasper J.F. van den Bosch

• Jen Evans

• Joan Massich

• Johan van der Meer

• Jona Sassenhagen

• Kambiz Tavabi

• Lorenz Esch

• Luke Bloy

• Mainak Jas

• Manu Sutela

• Marcin Koculak

• Marijn van Vliet

• Mikolaj Magnuski

• Peter J. Molfese

• Sam Perry

• Sara Sommariva

• Sergey Antopolskiy

• Sheraz Khan

• Stefan Appelhoff

• Stefan Repplinger

• Steven Bethard

• Teekuningas

• Teon Brooks

• Thomas Hartmann

• Thomas Jochmann

• Tom Dupré la Tour

• Tristan Stenner

• buildqa

• jeythekey

Version 0.16

Changelog

• Add possibility to pass dict of floats as argument to mne.make_ad_hoc_cov() by Nathalie Gayraud

• Add support for metadata in mne.Epochs by Chris Holdgraf, Alex Gramfort, Jona Sassenhagen, and Eric Larson

• Add support for plotting a dense head in mne.viz.plot_alignment() by Eric Larson

• Allow plotting in user-created mayavi Scene in mne.viz.plot_alignment() by Daniel McCloy

• Reduce memory consumption and do not require data to be loaded in mne.Epochs.apply_baseline() by Eric Larson

• Add option render_bem to mne.Report.parse_folder() by Eric Larson

• Add to mne.viz.plot_alignment() plotting of coordinate frame axes via show_axes and terrain-style interaction via interaction, by Eric Larson

• Add option initial_event to mne.find_events() by Clemens Brunner

• Left and right arrow keys now scroll by 25% of the visible data, whereas Shift+left/right scroll by a whole page in mne.io.Raw.plot() by Clemens Brunner

• Add support for gantry tilt angle determination from Elekta FIF file header by Chris Bailey

• Add possibility to concatenate mne.Annotations objects with + or += operators by Clemens Brunner

• Add support for MaxShield raw files in mne.Report by Eric Larson

• Add ability to plot whitened data in mne.io.Raw.plot(), mne.Epochs.plot(), mne.Evoked.plot(), and mne.Evoked.plot_topo() by Eric Larson

• Workaround for reading EGI MFF files with physiological signals that also present a bug from the EGI system in mne.io.read_raw_egi() by Federico Raimondo

• Add support for reading subject height and weight in info['subject_info'] by Eric Larson

• Improve online filtering of raw data when plotting with mne.io.Raw.plot() to filter in segments in accordance with the default skip_by_annotation=('edge', 'bad_acq_skip') of mne.io.Raw.filter() to avoid edge ringing by Eric Larson

• Add support for multiple head position files, plotting of sensors, and control of plotting color and axes in mne.viz.plot_head_positions() by Eric Larson

• Add ability to read and write Annotations separate from mne.io.Raw instances via Annotations.save() and read_annotations() by Eric Larson

• Add option to unset a montage by passing None to mne.io.Raw.set_montage() by Clemens Brunner

• Add sensor denoising via mne.preprocessing.oversampled_temporal_projection() by Eric Larson

• Add mne.io.pick.get_channel_types which returns all available channel types in MNE by Clemens Brunner

• Use standard PCA instead of randomized PCA whitening prior to ICA to increase reproducibility by Clemens Brunner

• Plot sEEG electrodes in mne.viz.plot_alignment() by Alex Gramfort

• Add support for any data type like sEEG or ECoG in covariance related functions (estimation, whitening and plotting) by Alex Gramfort and Eric Larson

• Add function mne.io.read_annotations_eeglab to allow loading annotations from EEGLAB files, by Alex Gramfort

• mne.io.Raw.set_montage() now accepts a string as its montage argument; this will set a builtin montage, by Clemens Brunner

• Add 4D BTi phantom dataset mne.datasets.phantom_4dbti.data_path(), by Alex Gramfort

• Changed the background color to grey in mne.viz.plot_alignment() to make helmet more visible, by Alex Gramfort

• Add mne.io.Raw.reorder_channels(), mne.Evoked.reorder_channels(), etc. to reorder channels, by Eric Larson

• Add to mne coreg and mne.gui.coregistration() by Eric Larson:

  • Improved visibility of points inside the head

  • Projection of EEG electrodes

  • Orientation of extra points toward the surface

  • Scaling points by distance to the head surface

  • Display of HPI points

  • ICP fitting with convergence criteria

  • Faster display updates

  • Scaling of mri/*.mgz files

  • Scaling of mri/trainsforms/talairach.xfm files for conversion to MNI space

• Add ability to exclude components interactively by clicking on their labels in mne.preprocessing.ICA.plot_components() by Mikołaj Magnuski

• Add reader for manual annotations of raw data produced by Brainstorm by Anne-Sophie Dubarry

• Add eLORETA noise normalization for minimum-norm solvers by Eric Larson

• Tighter duality gap computation in mne.inverse_sparse.tf_mxne_optim and new parametrization with alpha and l1_ratio instead of alpha_space and alpha_time by Mathurin Massias and Daniel Strohmeier

• Add dgap_freq parameter in mne.inverse_sparse.mxne_optim solvers to control the frequency of duality gap computation by Mathurin Massias and Daniel Strohmeier

• Add support for reading Eximia files by Eric Larson and Federico Raimondo

• Add the Picard algorithm to perform ICA for mne.preprocessing.ICA, by Pierre Ablin and Alex Gramfort

• Add ability to supply a mask to the plot in mne.viz.plot_evoked_image() by Jona Sassenhagen

• Add connectivity=False to cluster-based statistical functions to perform non-clustering stats by Eric Larson

• Add mne.time_frequency.csd_morlet() and mne.time_frequency.csd_array_morlet() to estimate cross-spectral density using Morlet wavelets, by Marijn van Vliet

• Add multidictionary time-frequency support to mne.inverse_sparse.tf_mixed_norm() by Mathurin Massias and Daniel Strohmeier

• Add new DICS implementation as mne.beamformer.make_dics(), mne.beamformer.apply_dics(), mne.beamformer.apply_dics_csd() and mne.beamformer.apply_dics_epochs(), by Marijn van Vliet and Susanna Aro

Bug

• Fix bug in EEG interpolation code to do nothing if there is no channel to interpolate by Mainak Jas

• Fix bug in mne.preprocessing.peak_finder to output datatype consistently and added input check for empty vectors by Tommy Clausner

• Fix bug in mne.io.read_raw_brainvision() to use the correct conversion for filters from time constant to frequency by Stefan Appelhoff

• Fix bug with events when saving split files using mne.Epochs.save() by Eric Larson

• Fix bug in mne.decoding.SlidingEstimator and mne.decoding.GeneralizingEstimator to allow mne.decoding.cross_val_multiscore() to automatically detect whether the base_estimator is a classifier and use a StratifiedKFold instead of a KFold when cv is not specified, by Jean-Remi King

• Fix bug in mne.set_eeg_reference() to remove an average reference projector when setting the reference to [] (i.e. do not change the existing reference) by Clemens Brunner

• Fix bug in threshold-free cluster enhancement parameter validation (mne.stats.permutation_cluster_1samp_test() and mne.stats.permutation_cluster_test()) by Clemens Brunner

• Fix bug in mne.io.Raw.plot() to correctly display event types when annotations are present by Clemens Brunner

• Fix bug in mne.stats.spatio_temporal_cluster_test() default value for threshold is now calculated based on the array sizes in X, by Eric Larson

• Fix bug in mne.simulation.simulate_raw() with use_cps=True where CPS was not actually used by Eric Larson

• Fix bug in mne.simulation.simulate_raw() where 1- and 3-layer BEMs were not properly transformed using trans by Eric Larson

• Fix bug in mne.viz.plot_alignment() where the head surface file -head.fif was not used even though present by Chris Bailey

• Fix bug when writing compressed sparse column matrices (e.g., Maxwell filtering cross-talk matrices) by Marijn van Vliet and Eric Larson

• Fix bug in mne.io.Raw.plot_psd() to correctly deal with reject_by_annotation=False by Clemens Brunner

• Fix bug in mne.make_fixed_length_events() when hitting corner case problems rounding to sample numbers by Eric Larson

• Fix bug in mne.Epochs when passing events as list with event_id=None by Alex Gramfort

• Fix bug in mne.Report.add_figs_to_section() when passing numpy.ndarray by Eric Larson

• Fix bug in CSS class setting in mne.Report BEM section by Eric Larson

• Fix bug in Annotations where annotations that extend to the end of a recording were not extended properly by Eric Larson

• Fix bug in mne.io.Raw.filter() to properly raw data with acquisition skips in separate segments by Eric Larson

• Fix bug in mne.preprocessing.maxwell_filter() where homogeneous fields were not removed for CTF systems by Eric Larson

• Fix computation of average quaternions in mne.preprocessing.maxwell_filter() by Eric Larson

• Fix bug in writing raw.annotations where empty annotations could not be written to disk, by Eric Larson

• Fix support for writing FIF files with acquisition skips by using empty buffers rather than writing zeros by Eric Larson

• Fix bug in the mne make_scalp_surfaces command where --force (to bypass topology check failures) was ignored by Eric Larson

• Fix bug in mne.preprocessing.maxwell_filter() when providing origin in 'meg' coordinate frame for recordings with a MEG to head transform (i.e., non empty-room recordings) by Eric Larson

• Fix bug in mne.viz.plot_cov() that ignored colorbar argument by Nathalie Gayraud

• Fix bug when picking CTF channels that could cause data saved to disk to be unreadable by Eric Larson

• Fix bug when reading event latencies (in samples) from eeglab files didn’t translate indices to 0-based python indexing by Mikołaj Magnuski

• Fix consistency between mne.Epochs and mne.stats.linear_regression_raw() in converting between samples and times (mne.stats.linear_regression_raw() now rounds, instead of truncating) by Phillip Alday

• Fix bug in mne coreg where sphere surfaces were scaled by Eric Larson

• Fix bug in mne.Evoked.plot_topomap() when using proj='interactive' mode by Eric Larson

• Fix bug when passing show_sensors=1 to mne.viz.plot_compare_evokeds() resulted in sensors legend placed in lower right of the figure (position 4 in matplotlib), not upper right by Mikołaj Magnuski

• Fix handling of annotations when cropping and concatenating raw data by Alex Gramfort and Eric Larson

• Fix bug in mne.preprocessing.create_ecg_epochs() where keep_ecg=False was ignored by Eric Larson

• Fix bug in mne.io.Raw.plot_psd() when picks is not None and picks spans more than one channel type by Eric Larson

• Fix bug in mne.make_forward_solution when passing data with compensation channels (e.g. CTF) that contain bad channels by Alex Gramfort

• Fix bug in mne.SourceEstimate.get_peak() and mne.VolSourceEstimate.get_peak() when there is only a single time point by Marijn van Vliet

• Fix bug in mne.io.read_raw_edf() when reading BDF files stimulus channels are now not scaled anymore by Clemens Brunner

API

• Channels with unknown locations are now assigned position [np.nan, np.nan, np.nan] instead of [0., 0., 0.], by Eric Larson

• Removed unused image_mask argument from mne.viz.plot_topomap() by Eric Larson

• Unknown measurement dates are now stored as info['meas_date'] = None rather than using the current date. None is also now used when anonymizing data and when determining the machine ID for writing files, by Mainak Jas and Eric Larson

• mne.Evoked.plot() will now append the number of epochs averaged for the evoked data in the first plot title, by Eric Larson

• Changed the line width in mne.viz.plot_bem() from 2.0 to 1.0 for better visibility of underlying structures, by Eric Larson

• Changed the behavior of mne.io.Raw.pick_channels() and similar methods to be consistent with mne.pick_channels() to treat channel list as a set (ignoring order) – if reordering is necessary use inst.reorder_channels, by Eric Larson

• Changed the labeling of some plotting functions to use more standard capitalization and units, e.g. “Time (s)” instead of “time [sec]” by Eric Larson

• mne.time_frequency.csd_epochs has been refactored into mne.time_frequency.csd_fourier() and mne.time_frequency.csd_multitaper(), by Marijn van Vliet

• mne.time_frequency.csd_array has been refactored into mne.time_frequency.csd_array_fourier() and mne.time_frequency.csd_array_multitaper(), by Marijn van Vliet

• Added clean_names=False parameter to mne.io.read_raw_ctf() for control over cleaning of main channel names and compensation channel names from CTF suffixes by Oleh Kozynets

• The functions lcmv, lcmv_epochs, and lcmv_raw are now deprecated in favor of mne.beamformer.make_lcmv() and mne.beamformer.apply_lcmv(), mne.beamformer.apply_lcmv_epochs(), and mne.beamformer.apply_lcmv_raw(), by Britta Westner

• The functions mne.beamformer.dics, mne.beamformer.dics_epochs and mne.beamformer.dics_source_power are now deprecated in favor of mne.beamformer.make_dics(), mne.beamformer.apply_dics(), and mne.beamformer.apply_dics_csd(), by Marijn van Vliet

Authors

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

• Alejandro Weinstein

• Alexandre Gramfort

• Annalisa Pascarella

• Anne-Sophie Dubarry

• Britta Westner

• Chris Bailey

• Chris Holdgraf

• Christian Brodbeck

• Claire Braboszcz

• Clemens Brunner

• Daniel McCloy

• Denis A. Engemann

• Desislava Petkova

• Dominik Krzemiński

• Eric Larson

• Erik Hornberger

• Fede Raimondo

• Henrich Kolkhorst

• Jean-Remi King

• Jen Evans

• Joan Massich

• Jon Houck

• Jona Sassenhagen

• Juergen Dammers

• Jussi Nurminen

• Kambiz Tavabi

• Katrin Leinweber

• Kostiantyn Maksymenko

• Larry Eisenman

• Luke Bloy

• Mainak Jas

• Marijn van Vliet

• Mathurin Massias

• Mikolaj Magnuski

• Nathalie Gayraud

• Oleh Kozynets

• Phillip Alday

• Pierre Ablin

• Stefan Appelhoff

• Stefan Repplinger

• Tommy Clausner

• Yaroslav Halchenko

Version 0.15

Changelog

• mne.channels.Layout.plot() and 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 mne.decoding.cross_val_multiscore() to allow scoring of multiple tasks, typically used with mne.decoding.SlidingEstimator, by Jean-Remi King

• Add mne.decoding.ReceptiveField module for modeling electrode response to input features by Chris Holdgraf

• Add mne.decoding.TimeDelayingRidge class, used by default by mne.decoding.ReceptiveField, to speed up auto- and cross-correlation computations and enable Laplacian regularization by Ross Maddox and Eric Larson

• Add new mne.datasets.mtrf dataset by Chris Holdgraf

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

• Add mne.decoding.SPoC to fit and apply spatial filters based on continuous target variables, by Jean-Remi King and Alexandre Barachant

• Add Fieldtrip’s electromyogram dataset, by Alexandre Barachant

• Add reject_by_annotation option to mne.preprocessing.find_eog_events() (which is also utilised by 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 mne.time_frequency.EpochsTFR.save() by Jaakko Leppakangas

• Add butterfly mode (toggled with ‘b’ key) to mne.io.Raw.plot() by Jaakko Leppakangas

• Add axes parameter to plot_topo functions by Jaakko Leppakangas

• Add options to change time windowing in mne.chpi.filter_chpi() by Eric Larson

• mne.channels.Montage.plot, mne.channels.DigMontage.plot(), and mne.viz.plot_montage() now allow plotting channel locations as a topomap by Clemens Brunner

• Add background_color parameter to mne.Evoked.plot_topo() and mne.viz.plot_evoked_topo() and improve axes rendering as done in mne.viz.plot_compare_evokeds() by Alex Gramfort

• Add support for GDF files in 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 mne.io.Raw.plot() and 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 Dipole objects in sparse source imaging methods by Daniel Strohmeier

• Add 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 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 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 mne.Report by Eric Larson

• Add confidence intervals, number of free parameters, and χ² to mne.fit_dipole() and mne.read_dipole() by Eric Larson

• mne.SourceEstimate.data is now writable, writing to it will also update mne.SourceEstimate.times by Marijn van Vliet

• mne.io.Raw.plot() and mne.Epochs.plot() now use anti-aliasing to draw signals by Clemens Brunner

• Allow using saved DigMontage to import digitization to mne.gui.coregistration() by Jaakko Leppakangas

• Add function mne.channels.get_builtin_montages() to list all built-in montages by Clemens Brunner

• mne.decoding.SlidingEstimator and mne.decoding.GeneralizingEstimator now accept **fit_params at fitting by Jean-Remi King

• Add mne.VectorSourceEstimate class which enables working with both source power and dipole orientations by Marijn van Vliet

• Add option pick_ori='vector' to mne.minimum_norm.apply_inverse() to produce mne.VectorSourceEstimate by Marijn van Vliet

• Add support for numpy.random.RandomState argument to seed in statistical clustering functions and better documentation of exact 1-sample tests by Eric Larson

• Extend mne.viz.plot_epochs_image()/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 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 (mne.viz.plot_raw() or 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 mne.Epochs.filter() and mne.Evoked.filter(), as well as pad argument to 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 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 mne.minimum_norm.apply_inverse() by Eric Larson

• Add return_drop_log to mne.preprocessing.compute_proj_eog() and 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 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 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 mne.io.Raw.filter() to include ref_meg channels by default by Eric Larson

• Fix mne.decoding.CSP order of spatial filter in patterns_ by Alexandre Barachant

• 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 mne.preprocessing.ICA.plot_properties() where merging gradiometers would fail by Jaakko Leppakangas

• Fix mne.viz.plot_sensors() to maintain proper aspect ratio by Eric Larson

• Fix mne.viz.plot_topomap() to allow 0 contours by Jaakko Leppakangas

• Fix mne.preprocessing.ICA source-picking to increase threshold for rank estimation to 1e-14 by Jesper Duemose Nielsen

• Fix mne.set_bipolar_reference() to support duplicates in anodes by Jean-Baptiste Schiratti and Alex Gramfort

• Fix visuals of mne.viz.plot_evoked() and a bug where ylim changes when using interactive topomap plotting by Jaakko Leppakangas

• Fix mne.Evoked.plot_topomap() when using the mask argument with paired gradiometers by Eric Larson

• Fix bug in mne.Label.fill() where an empty label raised an error, by Eric Larson

• Fix mne.io.read_raw_ctf() to also include the samples in the last block by Jaakko Leppakangas

• Fix mne.preprocessing.ICA.save() to close file before attempting to delete it when write fails by Jesper Duemose Nielsen

• Fix mne.simulation.simulate_evoked() to use nave parameter instead of snr, by Yousra Bekhti

• Fix mne.read_bem_surfaces() for BEM files missing normals by Christian Brodbeck

• Fix mne.transform_surface_to() to actually copy when copy=True by Eric Larson

• Fix 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 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 mne.viz.plot_montage() by Clemens Brunner

• Fix bug in to_data_frame where non-consecutive picks would make the function crash by Jaakko Leppakangas

• Fix channel picking and drop in mne.time_frequency.EpochsTFR by Lukáš Hejtmánek

• Fix mne.SourceEstimate.transform() to properly update mne.SourceEstimate.times by Marijn van Vliet

• Fix 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 mne.forward.restrict_forward_to_label() or mne.forward.restrict_forward_to_stc() by Marijn van Vliet

• Fix bug in mne.viz.plot_compare_evokeds() where truncate_yaxis was ignored (default is now False), by Jona Sassenhagen

• Fix bug in mne.viz.plot_evoked() where all xlabels were removed when using spatial_colors=True, by Jesper Duemose Nielsen

• Fix field mapping mne.make_field_map() and MEG bad channel interpolation functions (e.g., mne.Evoked.interpolate_bads()) to choose a better number of components during pseudoinversion when few channels are available, by Eric Larson

• Fix bug in mne.io.read_raw_brainvision(), changed default to read coordinate information if available and added test, by Jesper Duemose Nielsen

• Fix bug in mne.SourceEstimate.to_original_src() where morphing failed if two vertices map to the same target vertex, by Marijn van Vliet

• Fix mne.preprocessing.Xdawn to give verbose error messages about rank deficiency and handle transforming 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 mne.Epochs.resample() and mne.Evoked.resample() to be 'edge' by default, by Eric Larson

• Fix mne.inverse_sparse.mixed_norm(), mne.inverse_sparse.tf_mixed_norm() and mne.inverse_sparse.gamma_map() to work with volume source space and sphere head models in MEG by Alex Gramfort and Yousra Bekhti

• Fix 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 mne.gui.coregistration() by Eric Larson

• Fix resampling of events along with raw in mne.io.Raw() to now take into consideration the value of first_samp by Chris Bailey

• Fix labels of PSD plots in mne.viz.plot_raw_psd() by Alejandro Weinstein

• Fix depth weighting of sparse solvers (mne.inverse_sparse.mixed_norm(), mne.inverse_sparse.tf_mixed_norm() and mne.inverse_sparse.gamma_map()) with free orientation source spaces to improve orientation estimation by Alex Gramfort and Yousra Bekhti

• Fix the threshold in mne.beamformer.rap_music() to properly estimate the rank by Yousra Bekhti

• Fix treatment of vector inverse in mne.minimum_norm.apply_inverse_epochs() by Emily Stephen

• Fix 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 mne.simulation functions instead, by Eric Larson

• Add skip_by_annotation to mne.io.Raw.filter() to process data concatenated with e.g. 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 mne.preprocessing.ICA and related functions, by Stefan Repplinger and Eric Larson

• Add mne.beamformer.make_lcmv() and mne.beamformer.apply_lcmv(), mne.beamformer.apply_lcmv_epochs(), and 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 mne.beamformer.rap_music() consistent with the GOF of dipoles returned by mne.fit_dipole() by Alex Gramfort.

• mne.decoding.SlidingEstimator will now replace mne.decoding.TimeDecoding to make it generic and fully compatible with scikit-learn, by Jean-Remi King and Alex Gramfort

• mne.decoding.GeneralizingEstimator will now replace mne.decoding.GeneralizationAcrossTime to make it generic and fully compatible with scikit-learn, by Jean-Remi 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-Remi King and Alex Gramfort

• Add norm_trace parameter to control single-epoch covariance normalization in :class:mne.decoding.CSP, by Jean-Remi King

• Allow passing a list of channel names as show_names in function mne.viz.plot_sensors() and methods mne.Evoked.plot_sensors(), mne.Epochs.plot_sensors() and 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.

• 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

• 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

• mne.io.Raw.plot_psd() now rejects data annotated bad by default. Turn off with reject_by_annotation=False, by Eric Larson

• mne.set_eeg_reference() and the related methods (e.g., 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 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 mne.Epochs.load_data(), or that are read from disk, by Eric Larson

• mne.time_frequency.psd_welch() and 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 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. mne.time_frequency.tfr_array_morlet(), by Eric Larson

• Add patterns=False parameter in 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 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 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 mne.read_forward_solution() by Daniel Strohmeier

• 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

• 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 mne.viz.plot_raw_psd() has been relaxed from error to warning by Alejandro Weinstein

• Expose “rank” parameter in 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 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-Remi 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

Version 0.14

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-Remi 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-Remi 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-Remi 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-Remi 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-Remi 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-Remi 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-Remi 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

Version 0.13

Changelog

• Add new class AcqParserFIF to parse Elekta/Neuromag MEG acquisition info, allowing e.g. collecting epochs according to acquisition-defined averaging categories by Jussi Nurminen

• Adds automatic determination of FIR filter parameters filter_length, l_trans_bandwidth, and h_trans_bandwidth and adds phase argument in e.g. in mne.io.Raw.filter() by Eric Larson

• Adds faster n_fft='auto' option to mne.io.Raw.apply_hilbert() by Eric Larson

• Adds new function mne.time_frequency.csd_array to compute the cross-spectral density of multivariate signals stored in an array, by Nick Foti

• Add order params ‘selection’ and ‘position’ for mne.viz.plot_raw() to allow plotting of specific brain regions by Jaakko Leppakangas

• Added the ability to decimate mne.Evoked objects with mne.Evoked.decimate() by Eric Larson

• Add generic array-filtering function mne.filter.filter_data() by Eric Larson

• mne.viz.plot_trans now also shows head position indicators by Christian Brodbeck

• Add label center of mass function mne.Label.center_of_mass() by Eric Larson

• Added mne.viz.plot_ica_properties() that allows plotting of independent component properties similar to pop_prop in EEGLAB. Also mne.preprocessing.ICA has mne.preprocessing.ICA.plot_properties() method now. Added by Mikołaj Magnuski

• Add second-order sections (instead of (b, a) form) IIR filtering for reduced numerical error by Eric Larson

• Add interactive colormap option to image plotting functions by Jaakko Leppakangas

• Add support for the University of Maryland KIT system by Christian Brodbeck

• Add support for *.elp and *.hsp files to the KIT2FIFF converter and mne.channels.read_dig_montage by Teon Brooks and Christian Brodbeck

• Add option to preview events in the KIT2FIFF GUI by Christian Brodbeck

• Add approximation of size of io.Raw, Epochs, and Evoked in repr() by Eric Larson

• Add possibility to select a subset of sensors by lasso selector to mne.viz.plot_sensors() and mne.viz.plot_raw() when using order=’selection’ or order=’position’ by Jaakko Leppakangas

• Add the option to plot brain surfaces and source spaces to viz.plot_bem() by Christian Brodbeck

• Add the --filterchpi option to mne browse_raw, by Felix Raimundo

• Add the --no-decimate option to mne make_scalp_surfaces to skip the high-resolution surface decimation step, by Eric Larson

• Add new class mne.decoding.EMS to transform epochs with the event-matched spatial filters and add ‘cv’ parameter to mne.decoding.compute_ems(), by Jean-Remi King

• Added mne.time_frequency.EpochsTFR and average parameter in mne.time_frequency.tfr_morlet() and mne.time_frequency.tfr_multitaper() to compute time-frequency transforms on single trial epochs without averaging, by Jean-Remi King and Alex Gramfort

• Added mne.decoding.TimeFrequency to transform signals in scikit-learn pipelines, by Jean-Remi King

• Added mne.decoding.UnsupervisedSpatialFilter providing interface for scikit-learn decomposition algorithms to be used with MNE data, by Jean-Remi King and Asish Panda

• Added support for multiclass decoding in mne.decoding.CSP, by Jean-Remi King and Alexandre Barachant

• Components obtained from mne.preprocessing.ICA are now sorted by explained variance, by Mikołaj Magnuski

• Adding an EEG reference channel using mne.add_reference_channels() will now use its digitized location from the FIFF file, if present, by Chris Bailey

• Added interactivity to mne.preprocessing.ICA.plot_components() - passing an instance of io.Raw or Epochs in inst argument allows to open component properties by clicking on component topomaps, by Mikołaj Magnuski

• Adds new function mne.viz.plot_compare_evokeds() to show multiple evoked time courses at a single location, or the mean over a ROI, or the GFP, automatically averaging and calculating a CI if multiple subjects are given, by Jona Sassenhagen

• Added transform_into parameter into mne.decoding.CSP to retrieve the average power of each source or the time course of each source, by Jean-Remi King

• Added support for reading MaxShield (IAS) evoked data (e.g., from the acquisition machine) in mne.read_evokeds() by Eric Larson

• Added support for functional near-infrared spectroscopy (fNIRS) channels by Jaakko Leppakangas

• Added mne.io.Raw.acqparser convenience attribute for mne.AcqParserFIF by Eric Larson

• Added example of Representational Similarity Analysis, by Jean-Remi King

BUG

• Fixed a bug where selecting epochs using hierarchical event IDs (HIDs) was and-like instead of or-like. When doing e.g. epochs[('Auditory', 'Left')], previously all trials that contain 'Auditory' and 'Left' (like 'Auditory/Left') would be selected, but now any conditions matching 'Auditory' or 'Left' will be selected (like 'Auditory/Left', 'Auditory/Right', and 'Visual/Left'). This is now consistent with how epoch selection was done without HID tags, e.g. epochs[['a', 'b']] would select all epochs of type 'a' and type 'b'. By Eric Larson

• Fixed Infomax/Extended Infomax when the user provides an initial weights matrix by Jair Montoya Martinez

• Fixed the default raw FIF writing buffer size to be 1 second instead of 10 seconds by Eric Larson

• Fixed channel selection order when MEG channels do not come first in mne.preprocessing.maxwell_filter() by Eric Larson

• Fixed color ranges to correspond to the colorbar when plotting several time instances with mne.viz.plot_evoked_topomap() by Jaakko Leppakangas

• Added units to mne.io.read_raw_brainvision() for reading non-data channels and enable default behavior of inferring channel type by unit by Jaakko Leppakangas and Pablo-Arias

• Fixed minor bugs with mne.Epochs.resample() and mne.Epochs.decimate() by Eric Larson

• Fixed a bug where duplicate vertices were not strictly checked by mne.simulation.simulate_stc() by Eric Larson

• Fixed a bug where some FIF files could not be read with mne.io.show_fiff() by Christian Brodbeck and Eric Larson

• Fixed a bug where merge_grads=True causes mne.viz.plot_evoked_topo() to fail when plotting a list of evokeds by Jaakko Leppakangas

• Fixed a bug when setting multiple bipolar references with set_bipolar_reference() by Marijn van Vliet.

• Fixed image scaling in mne.viz.plot_epochs_image() when plotting more than one channel by Jaakko Leppakangas

• Fixed mne.preprocessing.Xdawn to fit shuffled epochs by Jean-Remi King

• Fixed a bug with channel order determination that could lead to an AssertionError when using mne.Covariance matrices by Eric Larson

• Fixed the check for CTF gradient compensation in mne.preprocessing.maxwell_filter() by Eric Larson

• Fixed the import of EDF files with encoding characters in mne.io.read_raw_edf() by Guillaume Dumas

• Fixed mne.Epochs to ensure that detrend parameter is not a boolean by Jean-Remi King

• Fixed bug with mne.realtime.FieldTripClient.get_data_as_epoch when picks=None which crashed the function by Mainak Jas

• Fixed reading of units in .elc montage files (from UnitsPosition field) so that mne.channels.Montage objects are now returned with the pos attribute correctly in meters, by Chris Mullins

• Fixed reading of BrainVision files by Phillip Alday:

• Greater support for BVA files, especially older ones: alternate text coding schemes with fallback to Latin-1 as well as units in column headers

• Use online software filter information when present

• Fix comparisons of filter settings for determining “strictest”/”weakest” filter

• Weakest filter is now used for heterogeneous channel filter settings, leading to more consistent behavior with filtering methods applied to a subset of channels (e.g. Raw.filter with picks != None).

• Fixed plotting and timing of Annotations and restricted addition of annotations outside data range to prevent problems with cropping and concatenating data by Jaakko Leppakangas

• Fixed ICA plotting functions to refer to IC index instead of component number by Andreas Hojlund and Jaakko Leppakangas

• Fixed bug with picks when interpolating MEG channels by Mainak Jas.

• Fixed bug in padding of Stockwell transform for signal of length a power of 2 by Johannes Niediek

API

• The add_eeg_ref argument in core functions like mne.io.read_raw_fif() and mne.Epochs has been deprecated in favor of using mne.set_eeg_reference() and equivalent instance methods like raw.set_eeg_reference(). In functions like mne.io.read_raw_fif() where the default in 0.13 and older versions is add_eeg_ref=True, the default will change to add_eeg_ref=False in 0.14, and the argument will be removed in 0.15.

• Multiple aspects of FIR filtering in MNE-Python has been refactored:

  1. New recommended defaults for l_trans_bandwidth='auto', h_trans_bandwidth='auto', and filter_length='auto'. This should generally reduce filter artifacts at the expense of slight decrease in effective filter stop-band attenuation. For details see Defaults in MNE-Python. The default values of l_trans_bandwidth=h_trans_bandwidth=0.5 and filter_length='10s' will change to 'auto' in 0.14.

  2. The filter_length=None option (i.e. use len(x)) has been deprecated.

  3. An improved phase='zero' zero-phase FIR filtering has been added. Instead of running the designed filter forward and backward, the filter is applied once and we compensate for the linear phase of the filter. The previous phase='zero-double' default will change to phase='zero' in 0.14.

  4. A warning is provided when the filter is longer than the signal of interest, as this is unlikely to produce desired results.

  5. Previously, if the filter was as long or longer than the signal of interest, direct FFT-based computations were used. Now a single code path (overlap-add filtering) is used for all FIR filters. This could cause minor changes in how short signals are filtered.

• Support for Python 2.6 has been dropped, and the minimum supported dependencies are NumPy 1.8, SciPy 0.12, and Matplotlib 1.3 by Eric Larson

• When CTF gradient compensation is applied to raw data, it is no longer reverted on save of mne.io.Raw.save() by Eric Larson

• Adds mne.time_frequency.csd_epochs to replace mne.time_frequency.csd_compute_epochs for naming consistency. mne.time_frequency.csd_compute_epochs is now deprecated and will be removed in mne 0.14, by Nick Foti

• Weighted addition and subtraction of Evoked as ev1 + ev2 and ev1 - ev2 have been deprecated, use explicit mne.combine_evoked(..., weights='nave') instead by Eric Larson

• Deprecated support for passing a list of filenames to mne.io.Raw constructor, use mne.io.read_raw_fif() and mne.concatenate_raws() instead by Eric Larson

• Added options for setting data and date formats manually in mne.io.read_raw_cnt() by Jaakko Leppakangas

• Now channels with units of ‘C’, ‘µS’, ‘uS’, ‘ARU’ and ‘S’ will be turned to misc by default in mne.io.read_raw_brainvision() by Jaakko Leppakangas

• Add mne.io.anonymize_info() function to anonymize measurements and add methods to mne.io.Raw, mne.Epochs and mne.Evoked, by Jean-Remi King

• Now it is possible to plot only a subselection of channels in mne.viz.plot_raw() by using an array for order parameter by Jaakko Leppakangas

• EOG channels can now be included when calling mne.preprocessing.ICA.fit() and a proper error is raised when trying to include unsupported channels by Alexander Rudiuk

• mne.concatenate_epochs() and mne.compute_covariance() now check to see if all Epochs instances have the same MEG-to-Head transformation, and errors by default if they do not by Eric Larson

• Added option to pass a list of axes to mne.viz.plot_epochs_image() by Mikołaj Magnuski

• Constructing IIR filters in mne.filter.construct_iir_filter() defaults to output='ba' in 0.13 but this will be changed to output='sos' by Eric Larson

• Add zorder parameter to mne.Evoked.plot() and derived functions to sort allow sorting channels by e.g. standard deviation, by Jona Sassenhagen

• The baseline parameter of mne.Epochs.apply_baseline() is set by default (None, 0), by Felix Raimundo

• Adds mne.Evoked.apply_baseline() to be consistent with mne.Epochs.apply_baseline(), by Felix Raimundo

• Deprecated the baseline parameter in mne.Evoked, by Felix Raimundo

• The API of mne.SourceEstimate.plot() and mne.viz.plot_source_estimates() has been updated to reflect current PySurfer 0.6 API. The config_opts parameter is now deprecated and will be removed in mne 0.14, and the default representation for time will change from ms to s in mne 0.14. By Christian Brodbeck

• The default dataset location has been changed from examples/ in the MNE-Python root directory to ~/mne_data in the user’s home directory, by Eric Larson

• A new option set_env has been added to mne.set_config() that defaults to False in 0.13 but will change to True in 0.14, by Eric Larson

• The compensation parameter in mne.io.read_raw_fif() has been deprecated in favor of the method mne.io.Raw.apply_gradient_compensation() by Eric Larson

• mne.decoding.EpochsVectorizer has been deprecated in favor of mne.decoding.Vectorizer by Asish Panda

• The epochs_data parameter has been deprecated in mne.decoding.CSP, in favour of the X parameter to comply to scikit-learn API, by Jean-Remi King

• Deprecated mne.time_frequency.cwt_morlet and mne.time_frequency.single_trial_power in favour of mne.time_frequency.tfr_morlet() with parameter average=False, by Jean-Remi King and Alex Gramfort

• Add argument mask_type to func:mne.read_events and func:mne.find_events to support MNE-C style of trigger masking by Teon Brooks and Eric Larson

• Extended Infomax is now the new default in mne.preprocessing.infomax() (extended=True), by Clemens Brunner

• mne.io.read_raw_eeglab() and mne.read_epochs_eeglab() now take additional argument uint16_codec that allows to define the encoding of character arrays in set file. This helps in rare cases when reading a set file fails with TypeError: buffer is too small for requested array. By Mikołaj Magnuski

• Added mne.decoding.TemporalFilter to filter data in scikit-learn pipelines, by Asish Panda

• mne.preprocessing.create_ecg_epochs() now includes all the channels when picks=None by Jaakko Leppakangas

• mne.set_eeg_reference() now allows moving from a custom to an average EEG reference by Marijn van Vliet

Authors

The committer list for this release is the following (sorted by alphabetical order):

• Alexander Rudiuk

• Alexandre Barachant

• Alexandre Gramfort

• Asish Panda

• Camilo Lamus

• Chris Holdgraf

• Christian Brodbeck

• Christopher J. Bailey

• Christopher Mullins

• Clemens Brunner

• Denis A. Engemann

• Eric Larson

• Federico Raimondo

• Félix Raimundo

• Guillaume Dumas

• Jaakko Leppakangas

• Jair Montoya

• Jean-Remi King

• Johannes Niediek

• Jona Sassenhagen

• Jussi Nurminen

• Keith Doelling

• Mainak Jas

• Marijn van Vliet

• Michael Krause

• Mikolaj Magnuski

• Nick Foti

• Phillip Alday

• Simon-Shlomo Poil

• Teon Brooks

• Yaroslav Halchenko

Version 0.12

Changelog

• Add overlay_times parameter to mne.viz.plot_epochs_image() to be able to display for example reaction times on top of the images, by Alex Gramfort

• Animation for evoked topomap in mne.Evoked.animate_topomap() by Jaakko Leppakangas

• Make mne.channels.find_layout() more robust for KIT systems in the presence of bad or missing channels by Jaakko Leppakangas

• Add raw movement compensation to mne.preprocessing.maxwell_filter() by Eric Larson

• Add mne.Annotations for for annotating segments of raw data by Jaakko Leppakangas

• Add reading of .fif file montages by Eric Larson

• Add system config utility mne.sys_info() by Eric Larson

• Automatic cross-validation and scoring metrics in mne.decoding.GeneralizationAcrossTime, by Jean-Remi King

• mne.decoding.GeneralizationAcrossTime accepts non-deterministic cross-validations, by Jean-Remi King

• Add plotting RMS of gradiometer pairs in mne.viz.plot_evoked_topo() by Jaakko Leppakangas

• Add regularization methods to mne.compute_raw_covariance() by Eric Larson.

• Add command mne show_info to quickly show the measurement info from a .fif file from the terminal by Alex Gramfort.

• Add creating forward operator for dipole object mne.make_forward_dipole() by Chris Bailey

• Add reading and estimation of fixed-position dipole time courses (similar to Elekta xfit) using mne.read_dipole() and mne.fit_dipole() by Eric Larson.

• Accept mne.decoding.GeneralizationAcrossTime’s scorer parameter to be a string that refers to a scikit-learn metric scorer by Asish Panda.

• Add method mne.Epochs.plot_image() calling mne.viz.plot_epochs_image() for better usability by Asish Panda.

• Add mne.io.read_raw_cnt() for reading Neuroscan CNT files by Jaakko Leppakangas

• Add decim parameter to mne.time_frequency.cwt_morlet, by Jean-Remi King

• Add method mne.Epochs.plot_topo_image() by Jaakko Leppakangas

• Add the ability to read events when importing raw EEGLAB files, by Jona Sassenhagen.

• Add function mne.viz.plot_sensors() and methods mne.Epochs.plot_sensors(), mne.io.Raw.plot_sensors() and mne.Evoked.plot_sensors() for plotting sensor positions and mne.viz.plot_layout() and mne.channels.Layout.plot() for plotting layouts by Jaakko Leppakangas

• Add epoch rejection based on annotated segments by Jaakko Leppakangas

• Add option to use new-style MEG channel names in mne.read_selection() by Eric Larson

• Add option for proj in mne.EpochsArray by Eric Larson

• Enable the usage of mne.viz.plot_topomap() with an mne.Info instance for location information, by Jona Sassenhagen.

• Add support for electrocorticography (ECoG) channel type by Eric Larson

• Add option for first_samp in mne.make_fixed_length_events() by Jon Houck

• Add ability to auto-scale channel types for mne.viz.plot_raw() and mne.viz.plot_epochs() and corresponding object plotting methods by Chris Holdgraf

BUG

• mne.time_frequency.compute_raw_psd, mne.time_frequency.compute_epochs_psd, mne.time_frequency.psd_multitaper(), and mne.time_frequency.psd_welch() no longer remove rows/columns of the SSP matrix before applying SSP projectors when picks are provided by Chris Holdgraf.

• mne.Epochs.plot_psd() no longer calls a Welch PSD, and instead uses a Multitaper method which is more appropriate for epochs. Flags for this function are passed to mne.time_frequency.psd_multitaper() by Chris Holdgraf

• Time-cropping functions (e.g., mne.Epochs.crop(), mne.Evoked.crop(), mne.io.Raw.crop(), mne.SourceEstimate.crop()) made consistent with behavior of tmin and tmax of mne.Epochs, where nearest sample is kept. For example, for MGH data acquired with sfreq=600.614990234, constructing Epochs(..., tmin=-1, tmax=1) has bounds +/-1.00064103, and now epochs.crop(-1, 1) will also have these bounds (previously they would have been +/-0.99897607). Time cropping functions also no longer use relative tolerances when determining the boundaries. These changes have minor effects on functions that use cropping under the hood, such as mne.compute_covariance() and mne.connectivity.spectral_connectivity(). Changes by Jaakko Leppakangas and Eric Larson

• Fix EEG spherical spline interpolation code to account for average reference by Mainak Jas

• MEG projectors are removed after Maxwell filtering by Eric Larson

• Fix mne.decoding.TimeDecoding to allow specifying clf by Jean-Remi King

• Fix bug with units (uV) in ‘Brain Vision Data Exchange Header File Version 1.0’ by Federico Raimondo

• Fix bug where mne.preprocessing.maxwell_filter() destination parameter did not properly set device-to-head transform by Eric Larson

• Fix bug in rank calculation of mne.utils.estimate_rank, mne.io.Raw.estimate_rank, and covariance functions where the tolerance was set to slightly too small a value, new ‘auto’ mode uses values from scipy.linalg.orth by Eric Larson.

• Fix bug when specifying irregular train_times['slices'] in mne.decoding.GeneralizationAcrossTime, by Jean-Remi King

• Fix colorbar range on norm data by Jaakko Leppakangas

• Fix bug in mne.preprocessing.run_ica, which used the ecg_criterion parameter for the EOG criterion instead of eog_criterion by Christian Brodbeck

• Fix normals in CTF data reader by Eric Larson

• Fix bug in mne.io.read_raw_ctf(), when omitting samples at the end by Jaakko Leppakangas

• Fix info['lowpass'] value for downsampled raw data by Eric Larson

• Remove measurement date from mne.Info in mne.io.Raw.anonymize() by Eric Larson

• Fix bug that caused synthetic ecg channel creation even if channel was specified for ECG peak detection in mne.preprocessing.create_ecg_epochs() by Jaakko Leppakangas

• Fix bug with vmin and vmax when None is passed in mne.viz.plot_topo_image_epochs() by Jaakko Leppakangas

• Fix bug with mne.label_sign_flip() (and mne.extract_label_time_course()) by Natalie Klein and Eric Larson

• Add copy parameter in mne.Epochs.apply_baseline() and mne.io.Raw.filter() methods by Jona Sassenhagen and Alex Gramfort

• Fix bug in mne.merge_events() when using replace_events=False by Alex Gramfort

• Fix bug in mne.Evoked type setting in mne.stats.linear_regression_raw() by Eric Larson

• Fix bug in mne.io.edf.RawEDF highpass filter setting to take max highpass to match warning message by Teon Brooks

• Fix bugs with coordinane frame adjustments in mne.viz.plot_trans by Eric Larson

• Fix bug in colormap selection in mne.Evoked.plot_projs_topomap() by Jaakko Leppakangas

• Fix bug in source normal adjustment that occurred when 1) patch information is available (e.g., when distances have been calculated) and 2) points are excluded from the source space (by inner skull distance) by Eric Larson

• Fix bug when merging info that has a field with list of dicts by Jaakko Leppakangas

• The BTi/4D reader now considers user defined channel labels instead of the hard-ware names, however only for channels other than MEG. By Denis Engemann and Alex Gramfort.

• The BTi reader mne.io.read_raw_bti() can now read 2500 system data, by Eric Larson

• Fix bug in mne.compute_raw_covariance() where rejection by non-data channels (e.g. EOG) was not done properly by Eric Larson.

• Change default scoring method of mne.decoding.GeneralizationAcrossTime and mne.decoding.TimeDecoding to estimate the scores within the cross-validation as in scikit-learn as opposed to across all cross-validated y_pred. The method can be changed with the score_mode parameter by Jean-Remi King

• Fix bug in mne.io.Raw.save() where, in rare cases, automatically split files could end up writing an extra empty file that wouldn’t be read properly by Eric Larson

• Fix :class:mne.realtime.StimServer by removing superfluous argument ip used while initializing the object by Mainak Jas.

• Fix removal of projectors in mne.preprocessing.maxwell_filter() in st_only=True mode by Eric Larson

API

• The default picks=None in mne.viz.plot_epochs_image() now only plots the first 5 channels, not all channels, by Jona Sassenhagen

• The mesh_color parameter in mne.viz.plot_dipole_locations() has been removed (use brain_color instead), by Marijn van Vliet

• Deprecated functions mne.time_frequency.compute_raw_psd and mne.time_frequency.compute_epochs_psd, replaced by mne.time_frequency.psd_welch() by Chris Holdgraf

• Deprecated function mne.time_frequency.multitaper_psd and replaced by mne.time_frequency.psd_multitaper() by Chris Holdgraf

• The y_pred attribute in mne.decoding.GeneralizationAcrossTime and mne.decoding.TimeDecoding is now a numpy array, by Jean-Remi King

• The mne.bem.fit_sphere_to_headshape() function now default to dig_kinds='auto' which will use extra digitization points, falling back to extra plus eeg digitization points if there not enough extra points are available.

• The mne.bem.fit_sphere_to_headshape() now has a units argument that should be set explicitly. This will default to units='mm' in 0.12 for backward compatibility but change to units='m' in 0.13.

• Added default parameters in Epochs class namely event_id=None, tmin=-0.2 and tmax=0.5.

• To unify and extend the behavior of mne.compute_raw_covariance() relative to mne.compute_covariance(), the default parameter tstep=0.2 now discards any epochs at the end of the mne.io.Raw instance that are not the full tstep duration. This will slightly change the computation of mne.compute_raw_covariance(), but should only potentially have a big impact if the mne.io.Raw instance is short relative to tstep and the last, too short (now discarded) epoch contained data inconsistent with the epochs that preceded it.

• The default picks=None in mne.io.Raw.filter() now picks eeg, meg, seeg, and ecog channels, by Jean-Remi King and Eric Larson

• EOG, ECG and EMG channels are now plotted by default (if present in data) when using mne.viz.plot_evoked() by Marijn van Vliet

• Replace pseudoinverse-based solver with much faster Cholesky solver in mne.stats.linear_regression_raw(), by Jona Sassenhagen.

• CTF data reader now reads EEG locations from .pos file as HPI points by Jaakko Leppakangas

• Subselecting channels can now emit a warning if many channels have been subselected from projection vectors. We recommend only computing projection vertors for and applying projectors to channels that will be used in the final analysis. However, after picking a subset of channels, projection vectors can be renormalized with mne.Info.normalize_proj() if necessary to avoid warnings about subselection. Changes by Eric Larson and Alex Gramfort.

• Rename and deprecate mne.Epochs.drop_bad_epochs to mne.Epochs.drop_bad(), and mne.Epochs.drop_epochs to mne.Epochs.drop() by Alex Gramfort.

• The C wrapper mne.do_forward_solution has been deprecated in favor of the native Python version mne.make_forward_solution() by Eric Larson

• The events parameter of mne.EpochsArray() is set by default to chronological time-samples and event values to 1, by Jean-Remi King

Authors

The committer list for this release is the following (preceded by number of commits):

• 348 Eric Larson

• 347 Jaakko Leppakangas

• 157 Alexandre Gramfort

• 139 Jona Sassenhagen

• 67 Jean-Remi King

• 32 Chris Holdgraf

• 31 Denis A. Engemann

• 30 Mainak Jas

• 16 Christopher J. Bailey

• 13 Marijn van Vliet

• 10 Mark Wronkiewicz

• 9 Teon Brooks

• 9 kaichogami

• 8 Clément Moutard

• 5 Camilo Lamus

• 5 mmagnuski

• 4 Christian Brodbeck

• 4 Daniel McCloy

• 4 Yousra Bekhti

• 3 Fede Raimondo

• 1 Jussi Nurminen

• 1 MartinBaBer

• 1 Mikolaj Magnuski

• 1 Natalie Klein

• 1 Niklas Wilming

• 1 Richard Höchenberger

• 1 Sagun Pai

• 1 Sourav Singh

• 1 Tom Dupré la Tour

• 1 jona-sassenhagen@

• 1 kambysese

• 1 pbnsilva

• 1 sviter

• 1 zuxfoucault

Version 0.11

Changelog

• Maxwell filtering (SSS) implemented in mne.preprocessing.maxwell_filter() by Mark Wronkiewicz as part of Google Summer of Code, with help from Samu Taulu, Jukka Nenonen, and Jussi Nurminen. Our implementation includes support for:

  • Fine calibration

  • Cross-talk correction

  • Temporal SSS (tSSS)

  • Head position translation

  • Internal component regularization

• Compensation for movements using Maxwell filtering on epoched data in mne.epochs.average_movements() by Eric Larson and Samu Taulu

• Add reader for Nicolet files in mne.io.read_raw_nicolet() by Jaakko Leppakangas

• Add FIFF persistence for ICA labels by Denis Engemann

• Display ICA labels in mne.viz.plot_ica_scores() and mne.viz.plot_ica_sources() (for evoked objects) by Denis Engemann

• Plot spatially color coded lines in mne.Evoked.plot() by Jona Sassenhagen and Jaakko Leppakangas

• Add reader for CTF data in mne.io.read_raw_ctf() by Eric Larson

• Add support for Brainvision v2 in mne.io.read_raw_brainvision() by Teon Brooks

• Improve speed of generalization across time mne.decoding.GeneralizationAcrossTime decoding up to a factor of seven by Jean-Remi King and Federico Raimondo and Denis Engemann.

• Add the explained variance for each principal component, explained_var, key to the mne.Projection by Teon Brooks

• Added methods mne.Epochs.add_eeg_average_proj, mne.io.Raw.add_eeg_average_proj, and mne.Evoked.add_eeg_average_proj to add an average EEG reference.

• Add reader for EEGLAB data in mne.io.read_raw_eeglab() and mne.read_epochs_eeglab() by Mainak Jas

BUG

• Fix bug that prevented homogeneous bem surfaces to be displayed in HTML reports by Denis Engemann

• Added safeguards against None and negative values in reject and flat parameters in mne.Epochs by Eric Larson

• Fix train and test time window-length in mne.decoding.GeneralizationAcrossTime by Jean-Remi King

• Added lower bound in mne.stats.linear_regression() on p-values p_val (and resulting mlog10_p_val) using double floating point arithmetic limits by Eric Larson

• Fix channel name pick in mne.Evoked.get_peak() method by Alex Gramfort

• Fix drop percentages to take into account ignore option in mne.viz.plot_drop_log() and mne.Epochs.plot_drop_log() by Eric Larson.

• mne.EpochsArray no longer has an average EEG reference silently added (but not applied to the data) by default. Use mne.EpochsArray.add_eeg_ref to properly add one.

• Fix mne.io.read_raw_ctf() to read n_samp_tot instead of n_samp by Jaakko Leppakangas

API

• mne.io.read_raw_brainvision() now has event_id argument to assign non-standard trigger events to a trigger value by Teon Brooks

• mne.read_epochs() now has add_eeg_ref=False by default, since average EEG reference can be added before writing or after reading using the method mne.Epochs.add_eeg_ref.

• mne.EpochsArray no longer has an average EEG reference silently added (but not applied to the data) by default. Use mne.EpochsArray.add_eeg_average_proj to properly add one.

Authors

The committer list for this release is the following (preceded by number of commits):

• 171 Eric Larson

• 117 Jaakko Leppakangas

• 58 Jona Sassenhagen

• 52 Mainak Jas

• 46 Alexandre Gramfort

• 33 Denis A. Engemann

• 28 Teon Brooks

• 24 Clemens Brunner

• 23 Christian Brodbeck

• 15 Mark Wronkiewicz

• 10 Jean-Remi King

• 5 Marijn van Vliet

• 3 Fede Raimondo

• 2 Alexander Rudiuk

• 2 emilyps14

• 2 lennyvarghese

• 1 Marian Dovgialo

Version 0.10

Changelog

• Add support for generalized M-way repeated measures ANOVA for fully balanced designs with mne.stats.f_mway_rm() by Denis Engemann

• Add epochs browser to interactively view and manipulate epochs with mne.viz.plot_epochs() by Jaakko Leppakangas

• Speed up TF-MxNE inverse solver with block coordinate descent by Daniel Strohmeier and Yousra Bekhti

• Speed up zero-phase overlap-add (default) filtering by a factor of up to 2 using linearity by Ross Maddox and Eric Larson

• Add support for scaling and adjusting the number of channels/time per view by Jaakko Leppakangas

• Add support to toggle the show/hide state of all sections with a single keypress (‘t’) in mne.Report by Mainak Jas

• Add support for BEM model creation mne.make_bem_model() by Eric Larson

• Add support for BEM solution computation mne.make_bem_solution() by Eric Larson

• Add ICA plotters for raw and epoch components by Jaakko Leppakangas

• Add new object mne.decoding.TimeDecoding for decoding sensors’ evoked response across time by Jean-Remi King

• Add command mne freeview_bem_surfaces to quickly check BEM surfaces with Freeview by Alex Gramfort.

• Add support for splitting epochs into multiple files in mne.Epochs.save() by Mainak Jas and Alex Gramfort

• Add support for jointly resampling a raw object and event matrix to avoid issues with resampling status channels by Marijn van Vliet

• Add new method mne.preprocessing.Xdawn for denoising and decoding of ERP/ERF by Alexandre Barachant

• Add support for plotting patterns/filters in mne.decoding.CSP and mne.decoding.LinearModel by Romain Trachel

• Add new object mne.decoding.LinearModel for decoding M/EEG data and interpreting coefficients of linear models with patterns attribute by Romain Trachel and Alex Gramfort

• Add support to append new channels to an object from a list of other objects by Chris Holdgraf

• Add interactive plotting of topomap from time-frequency representation by Jaakko Leppakangas

• Add plot_topo method to Evoked object by Jaakko Leppakangas

• Add fetcher mne.datasets.brainstorm for datasets used by Brainstorm in their tutorials by Mainak Jas

• Add interactive plotting of single trials by right clicking on channel name in epochs browser by Jaakko Leppakangas

• New logos and logo generation script by Daniel McCloy

• Add ability to plot topomap with a “skirt” (channels outside of the head circle) by Marijn van Vliet

• Add multiple options to ICA infomax and extended infomax algorithms (number of subgaussian components, computation of bias, iteration status printing), enabling equivalent computations to those performed by EEGLAB by Jair Montoya Martinez

• Add mne.Epochs.apply_baseline() method to Epochs objects by Teon Brooks

• Add preload argument to mne.read_epochs() to enable on-demand reads from disk by Eric Larson

• Big rewrite of simulation module by Yousra Bekhti, Mark Wronkiewicz, Eric Larson and Alex Gramfort. Allows to simulate raw with artifacts (ECG, EOG) and evoked data, exploiting the forward solution. See mne.simulation.simulate_raw(), mne.simulation.simulate_evoked() and mne.simulation.simulate_sparse_stc()

• Add mne.Epochs.load_data() method to mne.Epochs by Teon Brooks

• Add support for drawing topomaps by selecting an area in mne.Evoked.plot() by Jaakko Leppakangas

• Add support for finding peaks in evoked data in mne.Evoked.plot_topomap() by Jona Sassenhagen and Jaakko Leppakangas

• Add source space morphing in morph_source_spaces() and SourceEstimate.to_original_src() by Eric Larson and Denis Engemann

• Adapt corrmap function (Viola et al. 2009) to semi-automatically detect similar ICs across data sets by Jona Sassenhagen and Denis Engemann and Eric Larson

• Clarify docstring for mne.preprocessing.ICA by jeythekey

• New mne flash_bem command to compute BEM surfaces from Flash MRI images by Lorenzo Desantis, Alex Gramfort and Eric Larson. See mne.bem.make_flash_bem().

• New gfp parameter in mne.Evoked.plot() method to display Global Field Power (GFP) by Eric Larson.

• Add mne.Report.add_slider_to_section() methods to mne.Report by Teon Brooks

BUG

• Fix mne.io.add_reference_channels not setting info[nchan] correctly by Federico Raimondo

• Fix mne.stats.bonferroni_correction reject mask output to use corrected p-values by Denis Engemann

• Fix FFT filter artifacts when using short windows in overlap-add by Eric Larson

• Fix picking channels from forward operator could return a channel ordering different from info['chs'] by Chris Bailey

• Fix dropping of events after downsampling stim channels by Marijn van Vliet

• Fix scaling in :func:mne.viz.utils._setup_vmin_vmax by Jaakko Leppakangas

• Fix order of component selection in mne.decoding.CSP by Clemens Brunner

API

• Rename and deprecate mne.viz.plot_topo for mne.viz.plot_evoked_topo by Jaakko Leppakangas

• Deprecated mne.decoding.transformer.ConcatenateChannels and replaced by mne.decoding.EpochsVectorizer by Romain Trachel

• Deprecated lws and renamed ledoit_wolf for the reg argument in mne.decoding.CSP by Romain Trachel

• Redesigned and rewrote mne.Epochs.plot() (no backwards compatibility) during the GSOC 2015 by Jaakko Leppakangas, Mainak Jas, Federico Raimondo and Denis Engemann

• Deprecated and renamed mne.viz.plot_image_epochs for mne.plot.plot_epochs_image by Teon Brooks

• picks argument has been added to mne.time_frequency.tfr_morlet(), mne.time_frequency.tfr_multitaper() by Teon Brooks

• mne.io.Raw.preload_data has been deprecated for mne.io.Raw.load_data() by Teon Brooks

• RawBrainVision objects now always have event channel 'STI 014', and recordings with no events will have this channel set to zero by Eric Larson

Authors

The committer list for this release is the following (preceded by number of commits):

• 273 Eric Larson

• 270 Jaakko Leppakangas

• 194 Alexandre Gramfort

• 128 Denis A. Engemann

• 114 Jona Sassenhagen

• 107 Mark Wronkiewicz

• 97 Teon Brooks

• 81 Lorenzo De Santis

• 55 Yousra Bekhti

• 54 Jean-Remi King

• 48 Romain Trachel

• 45 Mainak Jas

• 40 Alexandre Barachant

• 32 Marijn van Vliet

• 26 Jair Montoya

• 22 Chris Holdgraf

• 16 Christopher J. Bailey

• 7 Christian Brodbeck

• 5 Natalie Klein

• 5 Fede Raimondo

• 5 Alan Leggitt

• 5 Roan LaPlante

• 5 Ross Maddox

• 4 Dan G. Wakeman

• 3 Daniel McCloy

• 3 Daniel Strohmeier

• 1 Jussi Nurminen

Version 0.9

Changelog

• Add support for mayavi figures in add_section method in Report by Mainak Jas

• Add extract volumes of interest from freesurfer segmentation and setup as volume source space by Alan Leggitt

• Add support to combine source spaces of different types by Alan Leggitt

• Add support for source estimate for mixed source spaces by Alan Leggitt

• Add SourceSpaces.save_as_volume method by Alan Leggitt

• Automatically compute proper box sizes when generating layouts on the fly by Marijn van Vliet

• Average evoked topographies across time points by Denis Engemann

• Add option to Report class to save images as vector graphics (SVG) by Denis Engemann

• Add events count to mne.viz.plot_events by Denis Engemann

• Add support for stereotactic EEG (sEEG) channel type by Marmaduke Woodman

• Add support for montage files by Denis Engemann, Marijn van Vliet, Jona Sassenhagen, Alex Gramfort and Teon Brooks

• Add support for spatiotemporal permutation clustering on sensors by Denis Engemann

• Add support for multitaper time-frequency analysis by Hari Bharadwaj

• Add Stockwell (S) transform for time-frequency representations by Denis Engemann and Alex Gramfort

• Add reading and writing support for time frequency data (AverageTFR objects) by Denis Engemann

• Add reading and writing support for digitizer data, and function for adding dig points to info by Teon Brooks

• Add plot_projs_topomap method to Raw, Epochs and Evoked objects by Teon Brooks

• Add EEG (based on spherical splines) and MEG (based on field interpolation) bad channel interpolation method to Raw, Epochs and Evoked objects by Denis Engemann and Mainak Jas

• Add parameter to whiten_evoked, compute_whitener and prepare_noise_cov to set the exact rank by Martin Luessi and Denis Engemann

• Add fiff I/O for processing history and MaxFilter info by Denis Engemann and Eric Larson

• Add automated regularization with support for multiple sensor types to compute_covariance by Denis Engemann and Alex Gramfort

• Add Evoked.plot_white method to diagnose the quality of the estimated noise covariance and its impact on spatial whitening by Denis Engemann and Alex Gramfort

• Add mne.evoked.grand_average function to compute grand average of Evoked data while interpolating bad EEG channels if necessary by Mads Jensen and Alex Gramfort

• Improve EEG referencing support and add support for bipolar referencing by Marijn van Vliet and Alex Gramfort

• Enable TFR calculation on Evoked objects by Eric Larson

• Add support for combining Evoked datasets with arbitrary weights (e.g., for oddball paradigms) by Eric Larson and Alex Gramfort

• Add support for concatenating a list of Epochs objects by Denis Engemann

• Labels support subtraction (label_1 - label_2) by Christian Brodbeck

• Add GeneralizationAcrossTime object with support for cross-condition generalization by Jean-Remi King and Denis Engemann

• Add support for single dipole fitting by Eric Larson

• Add support for spherical models in forward calculations by Eric Larson

• Add support for SNR estimation by Eric Larson

• Add support for Savitsky-Golay filtering of Evoked and Epochs by Eric Larson

• Add support for adding an empty reference channel to data by Teon Brooks

• Add reader function mne.io.read_raw_fif for Raw FIF files by Teon Brooks

• Add example of creating MNE objects from arbitrary data and NEO files by Jaakko Leppakangas

• Add plot_psd and plot_psd_topomap methods to epochs by Yousra Bekhti, Eric Larson and Denis Engemann

• evoked.pick_types, epochs.pick_types, and tfr.pick_types added by Eric Larson

• rename_channels and set_channel_types added as methods to Raw, Epochs and Evoked objects by Teon Brooks

• Add RAP-MUSIC inverse method by Yousra Bekhti and Alex Gramfort

• Add evoked.as_type to allow remapping data in MEG channels to virtual magnetometer or gradiometer channels by Mainak Jas

• Add mne.Report.add_bem_to_section(), mne.Report.add_htmls_to_section() methods to mne.Report by Teon Brooks

• Add support for KIT epochs files with read_epochs_kit by Teon Brooks

• Add whitening plots for evokeds to mne.Report by Mainak Jas

• Add DigMontage class and reader to interface with digitization info by Teon Brooks and Christian Brodbeck

• Add set_montage method to the Raw, Epochs, and Evoked objects by Teon Brooks and Denis Engemann

• Add support for capturing sensor positions when clicking on an image by Chris Holdgraf

• Add support for custom sensor positions when creating Layout objects by Chris Holdgraf

BUG

• Fix energy conservation for STFT with tight frames by Daniel Strohmeier

• Fix incorrect data matrix when tfr was plotted with parameters tmin, tmax, fmin and fmax by Mainak Jas

• Fix channel names in topomaps by Alex Gramfort

• Fix mapping of l_trans_bandwidth (to low frequency) and h_trans_bandwidth (to high frequency) in _BaseRaw.filter by Denis Engemann

• Fix scaling source spaces when distances have to be recomputed by Christian Brodbeck

• Fix repeated samples in client to FieldTrip buffer by Mainak Jas and Federico Raimondo

• Fix highpass and lowpass units read from Brainvision vhdr files by Alex Gramfort

• Add missing attributes for BrainVision and KIT systems needed for resample by Teon Brooks

• Fix file extensions of SSP projection files written by mne commands (from _proj.fif to -prof.fif) by Alex Gramfort

• Generating EEG layouts no longer requires digitization points by Marijn van Vliet

• Add missing attributes to BTI, KIT, and BrainVision by Eric Larson

• The API change to the edf, brainvision, and egi break backwards compatibility for when importing eeg data by Teon Brooks

• Fix bug in mne.viz.plot_topo if ylim was passed for single sensor layouts by Denis Engemann

• Average reference projections will no longer by automatically added after applying a custom EEG reference by Marijn van Vliet

• Fix picks argument to filter in n dimensions (affects FilterEstimator), and highpass filter in FilterEstimator by Mainak Jas

• Fix beamformer code LCMV/DICS for CTF data with reference channels by Denis Engemann and Alex Gramfort

• Fix scalings for bad EEG channels in mne.viz.plot_topo by Marijn van Vliet

• Fix EGI reading when no events are present by Federico Raimondo

• Add functionality to determine plot limits automatically or by data percentiles by Mark Wronkiewicz

• Fix bug in mne.io.edf where the channel offsets were omitted in the voltage calculations by Teon Brooks

• Decouple section ordering in command-line from python interface for mne-report by Mainak Jas

• Fix bug with ICA resetting by Denis Engemann

API

• apply_inverse functions have a new boolean parameter prepared which saves computation time by calling prepare_inverse_operator only if it is False

• find_events and read_events functions have a new parameter mask to set some bits to a don’t care state by Teon Brooks

• New channels module including layouts, electrode montages, and neighbor definitions of sensors which deprecates mne.layouts by Denis Engemann

• read_raw_brainvision, read_raw_edf, read_raw_egi all use a standard montage import by Teon Brooks

• Fix missing calibration factors for mne.io.egi.read_raw_egi by Denis Engemann and Federico Raimondo

• Allow multiple filename patterns as a list (e.g., *raw.fif and *-eve.fif) to be parsed by mne report in Report.parse_folder() by Mainak Jas

• read_hsp, read_elp, and write_hsp, write_mrk were removed and made private by Teon Brooks

• When computing the noise covariance or MNE inverse solutions, the rank is estimated empirically using more sensitive thresholds, which stabilizes results by Denis Engemann and Eric Larson and Alex Gramfort

• Raw FIFF files can be preloaded after class instantiation using raw.preload_data()

• Add label parameter to apply_inverse by Teon Brooks

• Deprecated label_time_courses for in_label method in SourceEstimate by Teon Brooks

• Deprecated as_data_frame for to_data_frame by Chris Holdgraf

• Add transform, unit parameters to read_montage by Teon Brooks

• Deprecated fmin, fmid, fmax in stc.plot and added clim by Mark Wronkiewicz

• Use scipy.signal.welch instead of matplotlib.psd inside compute_raw_psd and compute_epochs_psd by Yousra Bekhti Eric Larson and Denis Engemann. As a consquence, Raw.plot_raw_psds has been deprecated.

• Raw instances returned by mne.forward.apply_forward_raw now always have times starting from zero to be consistent with all other Raw instances. To get the former start and stop times, use raw.first_samp / raw.info['sfreq'] and raw.last_samp / raw.info['sfreq'].

• pick_types_evoked has been deprecated in favor of evoked.pick_types.

• Deprecated changing the sensor type of channels in rename_channels by Teon Brooks

• CUDA is no longer initialized at module import, but only when first used.

• add_figs_to_section and add_images_to_section now have a textbox parameter to add comments to the image by Teon Brooks

• Deprecated iir_filter_raw for fit_iir_model_raw.

• Add montage parameter to the create_info function to create the info using montages by Teon Brooks

Authors

The committer list for this release is the following (preceded by number of commits):

• 515 Eric Larson

• 343 Denis A. Engemann

• 304 Alexandre Gramfort

• 300 Teon Brooks

• 142 Mainak Jas

• 119 Jean-Remi King

• 77 Alan Leggitt

• 75 Marijn van Vliet

• 63 Chris Holdgraf

• 57 Yousra Bekhti

• 49 Mark Wronkiewicz

• 44 Christian Brodbeck

• 30 Jona Sassenhagen

• 29 Hari Bharadwaj

• 27 Clément Moutard

• 24 Ingoo Lee

• 18 Marmaduke Woodman

• 16 Martin Luessi

• 10 Jaakko Leppakangas

• 9 Andrew Dykstra

• 9 Daniel Strohmeier

• 7 kjs

• 6 Dan G. Wakeman

• 5 Federico Raimondo

• 3 Basile Pinsard

• 3 Christoph Dinh

• 3 Hafeza Anevar

• 2 Martin Billinger

• 2 Roan LaPlante

• 1 Manoj Kumar

• 1 Matt Tucker

• 1 Romain Trachel

• 1 mads jensen

• 1 sviter

Version 0.8

Changelog

• Add Python3 support by Nick Ward, Alex Gramfort, Denis Engemann, and Eric Larson

• Add get_peak method for evoked and stc objects by Denis Engemann

• Add iter_topography function for radically simplified custom sensor topography plotting by Denis Engemann

• Add field line interpolation by Eric Larson

• Add full provenance tacking for epochs and improve drop_log by Tal Linzen, Alex Gramfort and Denis Engemann

• Add systematic contains method to Raw, Epochs and Evoked for channel type membership testing by Denis Engemann

• Add fiff unicode writing and reading support by Denis Engemann

• Add 3D MEG/EEG field plotting function and evoked method by Denis Engemann and Alex Gramfort

• Add consistent channel-dropping methods to Raw, Epochs and Evoked by Denis Engemann and Alex Gramfort

• Add equalize_channnels function to set common channels for a list of Raw, Epochs, or Evoked objects by Denis Engemann

• Add plot_events function to visually display paradigm by Alex Gramfort

• Improved connectivity circle plot by Martin Luessi

• Add ability to anonymize measurement info by Eric Larson

• Add callback to connectivity circle plot to isolate connections to clicked nodes Roan LaPlante

• Add ability to add patch information to source spaces by Eric Larson

• Add split_label function to divide labels into multiple parts by Christian Brodbeck

• Add color attribute to Label objects by Christian Brodbeck

• Add max mode for extract_label_time_course by Mads Jensen

• Add rename_channels function to change channel names and types in info object by Dan Wakeman and Denis Engemann

• Add compute_ems function to extract the time course of experimental effects by Denis Engemann, Sébastien Marti and Alex Gramfort

• Add option to expand Labels defined in a source space to the original surface (Label.fill()) by Christian Brodbeck

• GUIs can be invoked form the command line using $ mne coreg and $ mne kit2fiff by Christian Brodbeck

• Add add_channels_epochs function to combine different recordings at the Epochs level by Christian Brodbeck and Denis Engemann

• Add support for EGI Netstation simple binary files by Denis Engemann

• Add support for treating arbitrary data (numpy ndarray) as a Raw instance by Eric Larson

• Support for parsing the EDF+ annotation channel by Martin Billinger

• Add EpochsArray constructor for creating epochs from numpy arrays by Denis Engemann and Federico Raimondo

• Add connector to FieldTrip realtime client by Mainak Jas

• Add color and event_id with legend options in plot_events in viz.py by Cathy Nangini

• Add events_list parameter to mne.concatenate_raws to concatenate events corresponding to runs by Denis Engemann

• Add read_ch_connectivity function to read FieldTrip neighbor template .mat files and obtain sensor adjacency matrices by Denis Engemann

• Add display of head in helmet from -trans.fif file to check coregistration quality by Mainak Jas

• Add raw.add_events to allow adding events to a raw file by Eric Larson

• Add plot_image method to Evoked object to display data as images by Jean-Remi King and Alex Gramfort and Denis Engemann

• Add BCI demo with CSP on motor imagery by Martin Billinger

• New ICA API with unified methods for processing Raw, Epochs and Evoked objects by Denis Engemann

• Apply ICA at the evoked stage by Denis Engemann

• New ICA methods for visualizing unmixing quality, artifact detection and rejection by Denis Engemann

• Add pick_channels and drop_channels mixin class to pick and drop channels from Raw, Epochs, and Evoked objects by Andrew Dykstra and Denis Engemann

• Add EvokedArray class to create an Evoked object from an array by Andrew Dykstra

• Add plot_bem method to visualize BEM contours on MRI anatomical images by Mainak Jas and Alex Gramfort

• Add automated ECG detection using cross-trial phase statistics by Denis Engemann and Juergen Dammers

• Add Forward class to succintly display gain matrix info by Andrew Dykstra

• Add reading and writing of split raw files by Martin Luessi

• Add OLS regression function by Tal Linzen, Teon Brooks and Denis Engemann

• Add computation of point spread and cross-talk functions for MNE type solutions by Alex Gramfort and Olaf Hauk

• Add mask parameter to plot_evoked_topomap and evoked.plot_topomap by Denis Engemann and Alex Gramfort

• Add infomax and extended infomax ICA by Denis Engemann, Juergen Dammers and Lukas Breuer and Federico Raimondo

• Aesthetically redesign interpolated topography plots by Denis Engemann and Alex Gramfort

• Simplify sensor space time-frequency analysis API with tfr_morlet function by Alex Gramfort and Denis Engemann

• Add new somatosensory MEG dataset with nice time-frequency content by Alex Gramfort

• Add HDF5 write/read support for SourceEstimates by Eric Larson

• Add InverseOperator class to display inverse operator info by Mainak Jas

• Add $ mne report command to generate html reports of MEG/EEG data analysis pipelines by Mainak Jas, Alex Gramfort and Denis Engemann

• Improve ICA verbosity with regard to rank reduction by Denis Engemann

BUG

• Fix incorrect times attribute when stc was computed using apply_inverse after decimation at epochs stage for certain, arbitrary sample frequencies by Denis Engemann

• Fix corner case error for step-down-in-jumps permutation test (when step-down threshold was high enough to include all clusters) by Eric Larson

• Fix selection of total number of components via float when picking ICA sources by Denis Engemann and Qunxi Dong

• Fix writing and reading transforms after modification in measurement info by Denis Engemann and Martin Luessi and Eric Larson

• Fix pre-whitening / rescaling when estimating ICA on multiple channels without covariance by Denis Engemann

• Fix ICA pre-whitening, avoid recomputation when applying ICA to new data by Denis Engemann

API

• The minimum numpy version has been increased to 1.6 from 1.4.

• Epochs object now has a selection attribute to track provenance of selected Epochs. The length of the drop_log attribute is now the same as the length of the original events passed to Epochs. In earlier versions it had the length of the events filtered by event_id. Epochs has also now a plot_drop_log method.

• Deprecate Epochs.drop_picks in favor of a new method called drop_channels

• Deprecate labels_from_parc and parc_from_labels in favor of read_labels_from_annot and write_labels_to_annot

• The default of the new add_dist option of setup_source_space to add patch information will change from False to True in MNE-Python 0.9

• Deprecate read_evoked and write_evoked in favor of read_evokeds and write_evokeds. read_evokeds will return all Evoked instances in a file by default.

• Deprecate setno in favor of condition in the initialization of an Evoked instance. This affects mne.fiff.Evoked and read_evokeds, but not read_evoked.

• Deprecate mne.fiff module, use mne.io instead e.g. mne.io.Raw instead of mne.fiff.Raw.

• Pick functions (e.g., pick_types) are now in the mne namespace (e.g. use mne.pick_types).

• Deprecated ICA methods specific to one container type. Use ICA.fit, ICA.get_sources ICA.apply and ICA.plot_* for processing Raw, Epochs and Evoked objects.

• The default smoothing method for mne.stc_to_label will change in v0.9, and the old method is deprecated.

• As default, for ICA the maximum number of PCA components equals the number of channels passed. The number of PCA components used to reconstruct the sensor space signals now defaults to the maximum number of PCA components estimated.

Authors

The committer list for this release is the following (preceded by number of commits):

• 418 Denis A. Engemann

• 284 Alexandre Gramfort

• 242 Eric Larson

• 155 Christian Brodbeck

• 144 Mainak Jas

• 49 Martin Billinger

• 49 Andrew Dykstra

• 44 Tal Linzen

• 37 Dan G. Wakeman

• 36 Martin Luessi

• 26 Teon Brooks

• 20 Cathy Nangini

• 15 Hari Bharadwaj

• 15 Roman Goj

• 10 Ross Maddox

• 9 Marmaduke Woodman

• 8 Praveen Sripad

• 8 Tanay

• 8 Roan LaPlante

• 5 Saket Choudhary

• 4 Nick Ward

• 4 Mads Jensen

• 3 Olaf Hauk

• 3 Brad Buran

• 2 Daniel Strohmeier

• 2 Federico Raimondo

• 2 Alan Leggitt

• 1 Jean-Remi King

• 1 Matti Hämäläinen

Version 0.7

Changelog

• Add capability for real-time feedback via trigger codes using StimServer and StimClient classes by Mainak Jas

• New decoding module for MEG analysis containing sklearn compatible transformers by Mainak Jas and Alex Gramfort

• New realtime module containing RtEpochs, RtClient and MockRtClient class by Martin Luessi, Christopher Dinh, Alex Gramfort, Denis Engemann and Mainak Jas

• Allow picking normal orientation in LCMV beamformers by Roman Goj, Alex Gramfort, Denis Engemann and Martin Luessi

• Add printing summary to terminal for measurement info by Denis Engemann

• Add read and write info attribute ICA objects by Denis Engemann

• Decoding with Common Spatial Patterns (CSP) by Romain Trachel and Alex Gramfort

• Add ICA plot_topomap function and method for displaying the spatial sensitivity of ICA sources by Denis Engemann

• Plotting multiple brain views at once by Eric Larson

• Reading head positions from raw FIFF files by Eric Larson

• Add decimation parameter to ICA.decompose* methods by Denis Engemann and Alex Gramfort

• Add rejection buffer to ICA.decompose* methods by Denis Engemann and Alex Gramfort

• Improve ICA computation speed and memory usage by Denis Engemann and Alex Gramfort

• Add polygonal surface decimation function to preprocess head surfaces for coregistration by Denis Engemann and Alex Gramfort

• DICS time-frequency beamforming for epochs, evoked and for estimating source power by Roman Goj, Alex Gramfort and Denis Engemann

• Add method for computing cross-spectral density (CSD) from epochs and class for storing CSD data by Roman Goj, Alex Gramfort and Denis Engemann

• Add trellis plot function and method for visualizing single epochs by Denis Engemann

• Add fiducials read/write support by Christian Brodbeck and Alex Gramfort

• Add select / drop bad channels in plot_raw on click by Denis Engemann

• Add ico and oct source space creation in native Python by Eric Larson

• Add interactive rejection of bad trials in plot_epochs by Denis Engemann

• Add morph map calculation by Eric Larson and Martin Luessi

• Add volume and discrete source space creation and I/O support by Eric Larson

• Time-frequency beamforming to obtain spectrograms in source space using LCMV and DICS by Roman Goj, Alex Gramfort and Denis Engemann

• Compute epochs power spectral density function by Denis Engemann

• Plot raw power spectral density by Eric Larson

• Computing of distances along the cortical surface by Eric Larson

• Add reading BEM solutions by Eric Larson

• Add forward solution calculation in native Python by Eric Larson

• Add (Neuro)debian license compatibility by Eric Larson

• Automatic QRS threshold selection for ECG events by Eric Larson

• Add Travis continuous integration service by Denis Engemann

• Add SPM face data set by Denis Engemann Martin Luessi and Alex Gramfort

• Support reading of EDF+,BDF data by Teon Brooks

• Tools for scaling MRIs (mne.scale_mri) by Christian Brodbeck

• GUI for head-MRI coregistration (mne.gui.coregistration) by Christian Brodbeck

• GUI for ki2fiff conversion (mne.gui.kit2fiff) by Christian Brodbeck

• Support reading of EEG BrainVision data by Teon Brooks

• Improve CTF compensation handling by Martin Luessi and Eric Larson

• Improve and extend automated layout guessing by Denis Engemann

• Add Continuum Analytics Anaconda support by Denis Engemann

• Add subtract evoked option to beamformers by Andrew Dykstra

• Add new transform method to SourceEstimate(s) by Andrew Dykstra

API

• The pick_normal parameter for minimum norm solvers has been renamed as pick_ori and normal orientation picking is now achieved by passing the value “normal” for the pick_ori parameter.

• ICA objects now expose the measurement info of the object fitted.

• Average EEG reference is now added by default to Raw instances.

• Removed deprecated read/write_stc/w, use SourceEstimate methods instead

• The chs argument in mne.layouts.find_layout is deprecated and will be removed in MNE-Python 0.9. Use info instead.

• plot_evoked and Epochs.plot now open a new figure by default. To plot on an existing figure please specify the axes parameter.

Authors

The committer list for this release is the following (preceded by number of commits):

• 336 Denis A. Engemann

• 202 Eric Larson

• 193 Roman Goj

• 138 Alexandre Gramfort

• 99 Mainak Jas

• 75 Christian Brodbeck

• 60 Martin Luessi

• 40 Teon Brooks

• 29 Romain Trachel

• 28 Andrew Dykstra

• 12 Mark Wronkiewicz

• 10 Christoph Dinh

• 8 Alan Leggitt

• 3 Yaroslav Halchenko

• 3 Daniel Strohmeier

• 2 Mads Jensen

• 2 Praveen Sripad

• 1 Luke Bloy

• 1 Emanuele Olivetti

• 1 Yousra BEKHTI

Version 0.6

Changelog

• Linear (and zeroth-order) detrending for Epochs and Evoked by Eric Larson

• Label morphing between subjects by Eric Larson

• Define events based on time lag between reference and target event by Denis Engemann

• ICA convenience function implementing an automated artifact removal workflow by Denis Engemann

• Bad channels no longer included in epochs by default by Eric Larson

• Support for diagonal noise covariances in inverse methods and rank computation by Eric Larson

• Support for using CUDA in FFT-based FIR filtering (method=’fft’) and resampling by Eric Larson

• Optimized FFT length selection for faster overlap-add filtering by Martin Luessi

• Ability to exclude bad channels from evoked plots or shown them in red by Martin Luessi

• Option to show both hemispheres when plotting SourceEstimate with PySurfer by Martin Luessi

• Optimized Raw reading and epoching routines to limit memory copies by Eric Larson

• Advanced options to save raw files in short or double precision by Eric Larson

• Option to detect decreasing events using find_events by Simon Kornblith

• Option to change default stim_channel used for finding events by Eric Larson

• Use average patch normal from surface-oriented forward solution in inverse calculation when possible by Eric Larson

• Function to plot drop_log from Epochs instance by Eric Larson

• Estimate rank of Raw data by Eric Larson

• Support reading of BTi/4D data by Denis Engemann

• Wrapper for generating forward solutions by Eric Larson

• Averaging forward solutions by Eric Larson

• Events now contain the pre-event stim channel value in the middle column, by Christian Brodbeck

• New function mne.find_stim_steps for finding all steps in a stim channel by Christian Brodbeck

• Get information about FIFF files using mne.fiff.show_fiff() by Eric Larson

• Compute forward fields sensitivity maps by Alex Gramfort and Eric Larson

• Support reading of KIT data by Teon Brooks and Christian Brodbeck

• Raw data visualization by Eric Larson

• Smarter SourceEstimate object that contains linear inverse kernel and sensor space data for fast time-frequency transforms in source space by Martin Luessi

• Add example of decoding/MVPA on MEG sensor data by Alex Gramfort

• Add support for non-paired tests in spatiotemporal cluster stats by Alex Gramfort

• Add unified SSP-projector API for Raw, Epochs and Evoked objects by Denis Engemann, Alex Gramfort Eric Larson and Martin Luessi

• Add support for delayed SSP application at evoked stage Denis Engemann, Alex Gramfort, Eric Larson and Martin Luessi

• Support selective parameter updating in functions taking dicts as arguments by Denis Engemann

• New ICA method sources_as_epochs to create Epochs in ICA space by Denis Engemann

• New method in Evoked and Epoch classes to shift time scale by Mainak Jas

• Added option to specify EOG channel(s) when computing PCA/SSP projections for EOG artifacts by Mainak Jas

• Improved connectivity interface to allow combinations of signals, e.g., seed time series and source estimates, by Martin Luessi

• Effective connectivity estimation using Phase Slope Index (PSI) by Martin Luessi

• Support for threshold-free cluster enhancement (TFCE) by Eric Larson

• Support for “hat” variance regularization by Eric Larson

• Access source estimates as Pandas DataFrame by Denis Engemann.

• Add example of decoding/MVPA on MEG source space data by Denis Engemann

• Add support for –tstart option in mne_compute_proj_eog.py by Alex Gramfort

• Add two-way repeated measures ANOVA for mass-univariate statistics by Denis Engemann, Eric Larson and Alex Gramfort

• Add function for summarizing clusters from spatio-temporal-cluster permutation tests by Denis Engemann and Eric Larson

• Add generator support for lcmv_epochs by Denis Engemann

• Gamma-MAP sparse source localization method by Martin Luessi and Alex Gramfort

• Add regular expression and substring support for selecting parcellation labels by Denis Engemann

• New plot_evoked option for interactive and reversible selection of SSP projection vectors by Denis Engemann

• Plot 2D flat topographies with interpolation for evoked and SSPs by Christian Brodbeck and Alex Gramfort

• Support delayed SSP applicationon for 2D flat topographies by Denis Engemann and Christian Brodbeck and Alex Gramfort

• Allow picking maximum power source, a.k.a. “optimal”, orientation in LCMV beamformers by Roman Goj, Alex Gramfort, Denis Engemann and Martin Luessi

• Add sensor type scaling parameter to plot_topo by Andrew Dykstra, Denis Engemann and Eric Larson

• Support delayed SSP application in plot_topo by Denis Engemann

API

• Deprecated use of fiff.pick_types without specifying exclude – use either [] (none), bads (bad channels), or a list of string (channel names).

• Depth bias correction in dSPM/MNE/sLORETA make_inverse_operator is now done like in the C code using only gradiometers if present, else magnetometers, and EEG if no MEG channels are present.

• Fixed-orientation inverse solutions need to be made using fixed=True option (using non-surface-oriented forward solutions if no depth weighting is used) to maintain compatibility with MNE C code.

• Raw.save() will only overwrite the destination file, if it exists, if option overwrite=True is set.

• mne.utils.set_config(), get_config(), get_config_path() moved to mne namespace.

• Raw constructor argument proj_active deprecated – use proj argument instead.

• Functions from the mne.mixed_norm module have been moved to the mne.inverse_sparse module.

• Deprecate CTF compensation (keep_comp and dest_comp) in Epochs and move it to Raw with a single compensation parameter.

• Remove artifacts module. Artifacts- and preprocessing related functions can now be found in mne.preprocessing.

Authors

The committer list for this release is the following (preceded by number of commits):

• 340 Eric Larson

• 330 Denis A. Engemann

• 204 Alexandre Gramfort

• 72 Christian Brodbeck

• 66 Roman Goj

• 65 Martin Luessi

• 37 Teon Brooks

• 18 Mainak Jas

• 9 Simon Kornblith

• 7 Daniel Strohmeier

• 6 Romain Trachel

• 5 Yousra BEKHTI

• 5 Brad Buran

• 1 Andrew Dykstra

• 1 Christoph Dinh

Version 0.5

Changelog

• Multi-taper PSD estimation for single epochs in source space using minimum norm by Martin Luessi

• Read and visualize .dip files obtained with xfit or mne_dipole_fit by Alex Gramfort

• Make EEG layout by Eric Larson

• Ability to specify SSP projectors when computing covariance from raw by Eric Larson

• Read and write txt based event files (.eve or .txt) by Eric Larson

• Pass qrs threshold to preprocessing functions by Eric Larson

• Compute SSP projections from continuous raw data by Eric Larson

• Support for applied SSP projections when loading Raw by Eric Larson and Alex Gramfort

• Support for loading Raw stored in different fif files by Eric Larson

• IO of many Evoked in a single fif file + compute Epochs.standard_error by Eric Larson and Alex Gramfort

• ICA computation on Raw and Epochs with automatic component selection by Denis Engemann and Alex Gramfort

• Saving ICA sources to fif files and creating ICA topography layouts by Denis Engemann

• Save and restore ICA session to and from fif by Denis Engemann

• Export raw, epochs and evoked data as data frame to the pandas library by Denis Engemann

• Export raw, epochs and evoked data to the nitime library by Denis Engemann

• Copy methods for raw and epochs objects by Denis Engemann, Martin Luessi and Alex Gramfort

• New raw objects method to get the time at certain indices by Denis Engemann and Alex Gramfort

• Plot method for evoked objects by Denis Engemann

• Enhancement of cluster-level stats (speed and memory efficiency) by Eric Larson and Martin Luessi

• Reading of source space distances by Eric Larson

• Support for filling / smoothing labels and speedup of morphing by Eric Larson

• Adding options for morphing by Eric Larson

• Plotting functions for time frequency and epochs image topographies by Denis Engemann and Alex Gramfort

• Plotting ERP/ERF images by Alex Gramfort

• See detailed subplot when cliking on a channel inside a topography plot by Martin Luessi, Eric Larson and Denis Engemann

• Misc channel type support plotting functions by Denis Engemann

• Improved logging support by Eric Larson

• Whitening of evoked data for plotting and quality checking by Alex Gramfort

• Transparent I/O of gzipped fif files (as .fif.gz) by Eric Larson

• Spectral connectivity estimation in sensor and source space by Martin Luessi

• Read and write Epochs in FIF files by Alex Gramfort

• Resampling of Raw, Epochs, and Evoked by Eric Larson

• Creating epochs objects for different conditions and accessing conditions via user-defined name by Denis Engemann , Eric Larson, Alex Gramfort and Christian Brodbeck

• Visualizing evoked responses from different conditions in one topography plot by Denis Engemann and Alex Gramfort

• Support for L21 MxNE solver using coordinate descent using scikit-learn by Alex Gramfort and Daniel Strohmeier

• Support IIR filters (butterworth, chebyshev, bessel, etc.) by Eric Larson

• Read labels from FreeSurfer parcellation by Martin Luessi

• Combining labels in source space by Christian Brodbeck

• Read and write source spaces, surfaces and coordinate transforms to and from files by Christian Brodbeck

• Downsample epochs by Christian Brodbeck and Eric Larson

• New labels class for handling source estimates by Christian Brodbeck, Martin Luessi and Alex Gramfort

• New plotting routines to easily display SourceEstimates using PySurfer by Alex Gramfort

• Function to extract label time courses from SourceEstimate(s) by Martin Luessi

• Function to visualize connectivity as circular graph by Martin Luessi and Alex Gramfort

• Time-frequency Mixed Norm Estimates (TF-MxNE) by Alex Gramfort and Daniel Strohmeier

API

• Added nave parameter to source_induced_power() and source_band_induced_power(), use nave=1 by default (wrong nave was used before).

• Use mne.layout.read_layout instead of mne.layout.Layout to read a layout file (.lout)

• Use raw.time_as_index instead of time_to_index (still works but is deprecated).

• The artifacts module (mne.artifacts) is now merged into mne.preprocessing

• Epochs objects now also take dicts as values for the event_id argument. They now can represent multiple conditions.

Authors

The committer list for this release is the following (preceded by number of commits):

• 313 Eric Larson

• 226 Alexandre Gramfort

• 219 Denis A. Engemann

• 104 Christian Brodbeck

• 85 Martin Luessi

• 6 Daniel Strohmeier

• 4 Teon Brooks

• 1 Dan G. Wakeman

Version 0.4

Changelog

• Add function to compute source PSD using minimum norm by Alex Gramfort

• L21 Mixed Norm Estimates (MxNE) by Alex Gramfort and Daniel Strohmeier

• Generation of simulated evoked responses by Alex Gramfort, Daniel Strohmeier, and Martin Luessi

• Fit AR models to raw data for temporal whitening by Alex Gramfort.

• speedup + reduce memory of mne.morph_data by Alex Gramfort.

• Backporting scipy.signal.firwin2 so filtering works with old scipy by Alex Gramfort.

• LCMV Beamformer for evoked data, single trials, and raw data by Alex Gramfort and Martin Luessi.

• Add support for reading named channel selections by Martin Luessi.

• Add Raw.filter method to more easily band pass data by Alex Gramfort.

• Add tmin + tmax parameters in mne.compute_covariance to estimate noise covariance in epochs baseline without creating new epochs by Alex Gramfort.

• Add support for sLORETA in apply_inverse, apply_inverse_raw, apply_inverse_epochs (API Change) by Alex Gramfort.

• Add method to regularize a noise covariance by Alex Gramfort.

• Read and write measurement info in forward and inverse operators for interactive visualization in mne_analyze by Alex Gramfort.

• New mne_compute_proj_ecg.py and mne_compute_proj_eog.py scripts to estimate ECG/EOG PCA/SSP vectors by Alex Gramfort and Martin Luessi.

• Wrapper function and script (mne_maxfilter.py) for Elekta Neuromag MaxFilter(TM) by Martin Luessi

• Add method to eliminate stimulation artifacts from raw data by linear interpolation or windowing by Daniel Strohmeier.

Authors

The committer list for this release is the following (preceded by number of commits):

• 118 Alexandre Gramfort

• 81 Martin Luessi

• 15 Daniel Strohmeier

• 4 Christian Brodbeck

• 4 Louis Thibault

• 2 Brad Buran

Version 0.3

Changelog

• Sign flip computation for robust label average of signed values by Alex Gramfort.

• Reading and writing of .w files by Martin Luessi.

• Support for modifying Raw object and allow raw data preloading with memory mapping by Martin Luessi and Alex Gramfort.

• Support of arithmetic of Evoked data (useful to concatenate between runs and compute contrasts) by Alex Gramfort.

• Support for computing sensor space data from a source estimate using an MNE forward solution by Martin Luessi.

• Support of arithmetic of Covariance by Alex Gramfort.

• Write BEM surfaces in Python by Alex Gramfort.

• Filtering operations and apply_function interface for Raw object by Martin Luessi.

• Support for complex valued raw fiff files and computation of analytic signal for Raw object by Martin Luessi.

• Write inverse operators (surface and volume) by Alex Gramfort.

• Covariance matrix computation with multiple event types by Martin Luessi.

• New tutorial in the documentation and new classes and functions reference page by Alex Gramfort.

Authors

The committer list for this release is the following (preceded by number of commits):

• 80 Alexandre Gramfort

• 51 Martin Luessi

Version 0.2

Changelog

• New stats functions for FDR correction and Bonferroni by Alex Gramfort.

• Faster time-frequency using downsampling trick by Alex Gramfort.

• Support for volume source spaces by Alex Gramfort (requires next MNE release or nightly).

• Improved Epochs handling by Martin Luessi (slicing, drop_bad_epochs).

• Bug fix in Epochs + ECG detection by Manfred Kitzbichler.

• New pick_types_evoked function by Alex Gramfort.

• SourceEstimate now supports algebra by Alex Gramfort.

API changes summary

Here are the code migration instructions when upgrading from mne-python version 0.1:

• New return values for the function find_ecg_events

Authors

The committer list for this release is the following (preceded by number of commits):

• 33 Alexandre Gramfort

• 12 Martin Luessi

• 2 Yaroslav Halchenko

• 1 Manfred Kitzbichler