Version 0.9 (2015-05-22)

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 consequence, 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