MNE-Python Code Updates¶

Changelog¶

• Automatically create a legend in mne.viz.evoked.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 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

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

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 :class: 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

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 lits 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 incuded 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

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 (#2758)
• 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 :class: 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 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

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

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 artefacts (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
• 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 :class: mne.decoding.transformer.ConcatenateChannels and replaced by :class: mne.decoding.transformer.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

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

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 measurment 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 Hamalainen

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 measurment 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

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

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

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

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

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