v0.8.rst

Version 0.8 (2014-06-25)

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-Rémi 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 succinctly display gain matrix info by `Andrew Dykstra`_
• Add reading and writing of split raw files by `Martin Luessi`_
• Add OLS regression function by `Tal Linzen`_, `Teon Brooks`_ and `Denis Engemann`_
• Add computation of point spread and cross-talk functions for MNE type solutions by `Alex Gramfort`_ and `Olaf Hauk`_
• Add mask parameter to plot_evoked_topomap and evoked.plot_topomap by `Denis Engemann`_ and `Alex Gramfort`_
• Add infomax and extended infomax ICA by `Denis Engemann`_, `Juergen Dammers`_ and `Lukas Breuer`_ and `Federico Raimondo`_
• Aesthetically redesign interpolated topography plots by `Denis Engemann`_ and `Alex Gramfort`_
• Simplify sensor space time-frequency analysis API with tfr_morlet function by `Alex Gramfort`_ and `Denis Engemann`_
• Add new somatosensory MEG dataset with nice time-frequency content by `Alex Gramfort`_
• Add HDF5 write/read support for SourceEstimates by `Eric Larson`_
• Add InverseOperator class to display inverse operator info by `Mainak Jas`_
• Add $ mne report command to generate html reports of MEG/EEG data analysis pipelines by `Mainak Jas`_, `Alex Gramfort`_ and `Denis Engemann`_
• Improve ICA verbosity with regard to rank reduction by `Denis Engemann`_

BUG

• Fix incorrect times attribute when stc was computed using apply_inverse after decimation at epochs stage for certain, arbitrary sample frequencies by `Denis Engemann`_
• Fix corner case error for step-down-in-jumps permutation test (when step-down threshold was high enough to include all clusters) by `Eric Larson`_
• Fix selection of total number of components via float when picking ICA sources by `Denis Engemann`_ and `Qunxi Dong`_
• Fix writing and reading transforms after modification in measurement info by `Denis Engemann`_ and `Martin Luessi`_ and `Eric Larson`_
• Fix pre-whitening / rescaling when estimating ICA on multiple channels without covariance by `Denis Engemann`_
• Fix ICA pre-whitening, avoid recomputation when applying ICA to new data by `Denis Engemann`_

API

• The minimum numpy version has been increased to 1.6 from 1.4.
• Epochs object now has a selection attribute to track provenance of selected Epochs. The length of the drop_log attribute is now the same as the length of the original events passed to Epochs. In earlier versions it had the length of the events filtered by event_id. Epochs has also now a plot_drop_log method.
• Deprecate Epochs.drop_picks in favor of a new method called drop_channels
• Deprecate labels_from_parc and parc_from_labels in favor of read_labels_from_annot and write_labels_to_annot
• The default of the new add_dist option of setup_source_space to add patch information will change from False to True in MNE-Python 0.9
• Deprecate read_evoked and write_evoked in favor of read_evokeds and write_evokeds. read_evokeds will return all Evoked instances in a file by default.
• Deprecate setno in favor of condition in the initialization of an Evoked instance. This affects mne.fiff.Evoked and read_evokeds, but not read_evoked.
• Deprecate mne.fiff module, use mne.io instead e.g. mne.io.Raw instead of mne.fiff.Raw.
• Pick functions (e.g., pick_types) are now in the mne namespace (e.g. use mne.pick_types).
• Deprecated ICA methods specific to one container type. Use ICA.fit, ICA.get_sources ICA.apply and ICA.plot_* for processing Raw, Epochs and Evoked objects.
• The default smoothing method for mne.stc_to_label will change in v0.9, and the old method is deprecated.
• As default, for ICA the maximum number of PCA components equals the number of channels passed. The number of PCA components used to reconstruct the sensor space signals now defaults to the maximum number of PCA components estimated.

Authors

The committer list for this release is the following (preceded by number of commits):

• 418 Denis A. Engemann
• 284 Alexandre Gramfort
• 242 Eric Larson
• 155 Christian Brodbeck
• 144 Mainak Jas
• 49 Martin Billinger
• 49 Andrew Dykstra
• 44 Tal Linzen
• 37 Dan G. Wakeman
• 36 Martin Luessi
• 26 Teon Brooks
• 20 Cathy Nangini
• 15 Hari Bharadwaj
• 15 Roman Goj
• 10 Ross Maddox
• 9 Marmaduke Woodman
• 8 Praveen Sripad
• 8 Tanay
• 8 Roan LaPlante
• 5 Saket Choudhary
• 4 Nick Ward
• 4 Mads Jensen
• 3 Olaf Hauk
• 3 Brad Buran
• 2 Daniel Strohmeier
• 2 Federico Raimondo
• 2 Alan Leggitt
• 1 Jean-Rémi King
• 1 Matti Hämäläinen