v0.10.rst

Version 0.10 (2015-10-26)

Changelog

• Add support for generalized M-way repeated measures ANOVA for fully balanced designs with :func:`mne.stats.f_mway_rm` by `Denis Engemann`_
• Add epochs browser to interactively view and manipulate epochs with :func:`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 :class:`mne.Report` by `Mainak Jas`_
• Add support for BEM model creation :func:`mne.make_bem_model` by `Eric Larson`_
• Add support for BEM solution computation :func:`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-Rémi 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 :func:`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 :class:`mne.preprocessing.Xdawn` for denoising and decoding of ERP/ERF by `Alexandre Barachant`_
• Add support for plotting patterns/filters in :class:`mne.decoding.CSP` and :class:`mne.decoding.LinearModel` by `Romain Trachel`_
• Add new object :class:`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 :mod:`mne.datasets.brainstorm <mne.datasets>` 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 :func:`mne.Epochs.apply_baseline` method to Epochs objects by `Teon Brooks`_
• Add preload argument to :func:`mne.read_epochs` to enable on-demand reads from disk by `Eric Larson`_
• Big rewrite of simulation module by `Yousra Bekhti`_, `Mark Wronkiewicz`_, `Eric Larson`_ and `Alex Gramfort`_. Allows to simulate raw with artifacts (ECG, EOG) and evoked data, exploiting the forward solution. See :func:`mne.simulation.simulate_raw`, :func:`mne.simulation.simulate_evoked` and :func:`mne.simulation.simulate_sparse_stc`
• Add :func:`mne.Epochs.load_data` method to :class:`mne.Epochs` by `Teon Brooks`_
• Add support for drawing topomaps by selecting an area in :func:`mne.Evoked.plot` by `Jaakko Leppakangas`_
• Add support for finding peaks in evoked data in :func:`mne.Evoked.plot_topomap` by `Jona Sassenhagen`_ and `Jaakko Leppakangas`_
• Add source space morphing in :func:`morph_source_spaces` and :func:`SourceEstimate.to_original_src` by `Eric Larson`_ and `Denis Engemann`_
• Adapt corrmap function (Viola et al. 2009) to semi-automatically detect similar ICs across data sets by `Jona Sassenhagen`_ and `Denis Engemann`_ and `Eric Larson`_
• Clarify docstring for :class:`mne.preprocessing.ICA` by `jeythekey`_
• New mne flash_bem command to compute BEM surfaces from Flash MRI images by `Lorenzo Desantis`_, `Alex Gramfort`_ and `Eric Larson`_. See :func:`mne.bem.make_flash_bem`.
• New gfp parameter in :func:`mne.Evoked.plot` method to display Global Field Power (GFP) by `Eric Larson`_.
• Add mne.Report.add_slider_to_section methods to :class:`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 mne.viz.utils._setup_vmin_vmax by `Jaakko Leppakangas`_
• Fix order of component selection in :class:`mne.decoding.CSP` by `Clemens Brunner`_

API

• Rename and deprecate mne.viz.plot_topo for mne.viz.plot_evoked_topo by `Jaakko Leppakangas`_
• Deprecated mne.decoding.transformer.ConcatenateChannels and replaced by mne.decoding.EpochsVectorizer by `Romain Trachel`_
• Deprecated lws and renamed ledoit_wolf for the reg argument in :class:`mne.decoding.CSP` by `Romain Trachel`_
• Redesigned and rewrote :meth:`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 :func:`mne.time_frequency.tfr_morlet`, :func:`mne.time_frequency.tfr_multitaper` by `Teon Brooks`_
• mne.io.Raw.preload_data has been deprecated for :func:`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-Rémi 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