v1.5.rst

Version 1.5.0 (2023-08-14)

Enhancements

• Add reader for NSx files (Blackrock Microsystems Data Acquisition Systems) (:gh:`11432` by :newcontrib:`Proloy Das`)
• Add cmap argument for the :func:`mne.viz.plot_sensors` (:gh:`11720` by :newcontrib:`Gennadiy Belonosov`)
• Return unmodified instance if new sampling frequency is identical to the original in :meth:`mne.io.Raw.resample`, :meth:`mne.Epochs.resample`, :meth:`mne.Evoked.resample` and :meth:`mne.SourceEstimate.resample` (:gh:`11736` by :newcontrib:`Gennadiy Belonosov`)
• When failing to locate a file, we now print the full path in quotation marks to help spot accidentally added trailing spaces (:gh:`11718` by `Richard Höchenberger`_)
• Add standard montage lookup table for easycap-M43 (:gh:`11744` by :newcontrib:`Diptyajit Das`)
• Added :class:`mne.preprocessing.eyetracking.Calibration` to store eye-tracking calibration info, and :func:`mne.preprocessing.eyetracking.read_eyelink_calibration` to read calibration data from EyeLink systems (:gh:`11719` by `Scott Huberty`_)
• Ocular :class:`mne.Annotations` read in by :func:`mne.io.read_raw_eyelink` are now channel aware. This means if the left eye blinked, the associated annotation will store this in the 'ch_names' key. (:gh:`11746` by `Scott Huberty`_)
• Added :func:`mne.preprocessing.eyetracking.interpolate_blinks` to linear interpolate eyetrack signals during blink periods. (:gh:`11740` by `Scott Huberty`_)
• Added a section for combining eye-tracking and EEG data to the preprocessing tutorial "working with eye tracker data in MNE-Python" (:gh:`11770` by `Scott Huberty`_)
• Added a show_bytes option to :ref:`mne show_fiff` to show byte offsets (:gh:`11800` by `Eric Larson`_)
• Add :meth:`mne.Annotations.count` and :func:`mne.count_annotations` to count unique annotations (:gh:`11796` by `Clemens Brunner`_)
• Split the display of :meth:`mne.preprocessing.ICA.plot_overlay` between sensor types and display the RMS for MEG sensors and the :term:`GFP` for EEG sensors in the second panel instead of the channel average (:gh:`11830` by `Mathieu Scheltienne`_)
• Add :meth:`mne.Info.set_channel_types`, :meth:`mne.Info.rename_channels`, :meth:`mne.Info.plot_sensors`, :meth:`mne.Info.anonymize`, :meth:`mne.Info.set_meas_date` (:gh:`11839` by `Alex Rockhill`_)
• Curry and NEDF raw files can now also be read with the generic :func:`mne.io.read_raw` function (:gh:`11841` by `Richard Höchenberger`_)

Bugs

• Fix bug in :func:`mne.bem.convert_flash_mris` to handle missing "flash5_reg.mgz" when processing "flash30" data. (:gh:`11842` by :newcontrib:`Hamza Abdelhedi`)
• Fix bug where epochs event_id was not kept by :func:`mne.channels.combine_channels` (:gh:`11786` by :newcontrib:`Samuel Louviot`)
• Fix bug where user-provided codec was not used to read annotations when loading EEGLAB .set files (:gh:`11773` by :newcontrib:`Yiping Zuo`)
• Fix bug that required curv.*h files to create Brain object (:gh:`11704` by :newcontrib:`Aaron Earle-Richardson`)
• Extended test to highlight bug in :func:`mne.stats.permutation_t_test` (:gh:`11575` by :newcontrib:`Joshua Calder-Travis`)
• Fix bug that used wrong indices for line/label styles (sometimes causing an IndexError) in :meth:`mne.preprocessing.ICA.plot_sources` under certain conditions (:gh:`11808` by :newcontrib:`Joshua Calder-Travis`)
• Fix bug with :func:`~mne.io.read_raw_snirf` to handle files with measurement time containing milliseconds (:gh:`11804` by :newcontrib:`Daniel Tse`)
• Fix loading of EDF with mixed sampling frequencies with :func:`mne.io.read_raw_edf`: Upsampling is now applied to the entire signal and no longer block based, significantly reducing edge artifacts (:gh:`11549` by `Simon Kern`_)
• Fix bug where :func:`mne.io.read_raw_cnt` imports unnecessary durations (:gh:`11828` by `Jacob Woessner`_)
• Fix bug where :meth:`mne.viz.Brain.add_volume_labels` used an incorrect orientation (:gh:`11730` by `Alex Rockhill`_)
• Fix bug with :func:`mne.forward.restrict_forward_to_label` where cortical patch information was not adjusted (:gh:`11694` by `Eric Larson`_)
• Fix bug with PySide6 compatibility (:gh:`11721` by `Eric Larson`_)
• Fix bug with :class:`mne.io.Raw`, :class:`mne.SourceEstimate`, and related classes where the decimate and shift_time methods were errantly added (:gh:`11853` by `Eric Larson`_)
• Fix hanging interpreter with matplotlib figures using mne/viz/_mpl_figure.py in spyder console and jupyter notebooks (:gh:`11696` by `Mathieu Scheltienne`_)
• Fix bug with overlapping text for :meth:`mne.Evoked.plot` (:gh:`11698` by `Alex Rockhill`_)
• Fix bug with :func:`mne.preprocessing.corrmap` where the template iteration had non-standard map averaging (:gh:`11857` by `Eric Larson`_)
• For :func:`mne.io.read_raw_eyelink`, the default value of the gap_description parameter is now 'BAD_ACQ_SKIP', following MNE convention (:gh:`11719` by `Scott Huberty`_)
• Fix bug with :func:`mne.io.read_raw_fil` where datasets without sensor positions would not import (:gh:`11733` by `George O'Neill`_)
• Fix bug with :func:`mne.chpi.compute_chpi_snr` where cHPI being off for part of the recording or bad channels being defined led to an error or incorrect behavior (:gh:`11754`, :gh:`11755` by `Eric Larson`_)
• Allow int-like for the argument id of ~mne.make_fixed_length_events (:gh:`11748` by `Mathieu Scheltienne`_)
• Fix bugs with :mod:`mne.decoding` classes (:gh:`11846` by `Eric Larson`_): - :class:`mne.decoding.ReceptiveField` now sets rf.fit_intercept_ during fit() rather than overwriting rf.fit_intercept - :class:`mne.decoding.SlidingEstimator` now returns the same dtype as X (usually float64) in sl.transform(X) rather than always returning int
• Fix bug with :func:`mne.beamformer.make_lcmv` where the source space was not checked properly when the label argument was provided (:gh:`11852` by `Eric Larson`_)
• Fix bug where :func:`mne.io.read_raw_egi` did not properly set the EEG reference location for the reference channel itself (:gh:`11822` by `Eric Larson`_)
• Fix bug with legacy :meth:`~mne.io.Raw.plot_psd` method where passed axes were not used (:gh:`11778` by `Daniel McCloy`_)
• blink :class:`mne.Annotations` read in by :func:`mne.io.read_raw_eyelink` now begin with 'BAD_', i.e. 'BAD_blink', because ocular data are missing during blinks. (:gh:`11746` by `Scott Huberty`_)
• Fix bug where :ref:`mne show_fiff` could fail with an ambiguous error if the file is corrupt (:gh:`11800` by `Eric Larson`_)
• Fix bug where annotation FIF files lacked an end block tag (:gh:`11800` by `Eric Larson`_)
• Fix display of :class:`~mne.Annotations` in mne.preprocessing.ICA.plot_sources when the raw has raw.first_samp != 0 and doesn't have a measurement date (:gh:`11766` by `Mathieu Scheltienne`_)
• Fix bug in read_raw_eyelink, where STATUS information of samples was always assumed to be in the file. Performance and memory improvements were also made. (:gh:`11823` by `Scott Huberty`_)
• Fix closing of a topographic map created from an interactive drag on an Evoked or PSD plot (:gh:`11862` by `Mathieu Scheltienne`_)

API changes

• The baseline argument can now be array-like (e.g. list, tuple, np.ndarray, ...) instead of only a tuple (:gh:`11713` by `Clemens Brunner`_)
• The events and event_id parameters of :meth:`Epochs.plot() <mne.Epochs.plot>` now accept boolean values; see docstring for details (:gh:`11445` by `Daniel McCloy`_ and `Clemens Brunner`_)
• Deprecated gap_description keyword argument of :func:`mne.io.read_raw_eyelink`, which will be removed in mne version 1.6, in favor of using :meth:`mne.Annotations.rename` (:gh:`11719` by `Scott Huberty`_)

Authors

• Aaron Earle-Richardson+
• Alex Rockhill
• Alexandre Gramfort
• Britta Westner
• Clemens Brunner
• Daniel McCloy
• Daniel Tse+
• Diptyajit Das+
• Eric Larson
• Gennadiy Belonosov+
• George O'Neill
• Hamza Abdelhedi+
• Jacob Woessner
• Joshua Calder-Travis+
• Mathieu Scheltienne
• Proloy Das
• Richard Höchenberger
• Rob Luke
• Samuel Louviot+
• Scott Huberty
• Simon Kern
• Stefan Appelhoff
• Thomas Moreau
• Yiping Zuo+