v1.4.rst

Version 1.4.0 (2023-05-10)

Enhancements

• Add functionality for reading CNT spans/annotations marked bad to :func:`mne.io.read_raw_cnt` (:gh:`11631` by :newcontrib:`Jacob Woessner`)
• Add :unit: Sphinx directive to enable use of uniform non-breaking spaces throughout the documentation (:gh:`11469` by :newcontrib:`Sawradip Saha`)
• Adjusted the algorithm used in :class:`mne.decoding.SSD` to support non-full rank data (:gh:`11458` by :newcontrib:`Thomas Binns`)
• Changed suggested type for ch_groups in mne.viz.plot_sensors from array to list of list(s) (arrays are still supported). (:gh:`11465` by `Hyonyoung Shin`_)
• Add support for UCL/FIL OPM data using :func:`mne.io.read_raw_fil` (:gh:`11366` by :newcontrib:`George O'Neill` and `Robert Seymour`_)
• Add harmonic field correction (HFC) for OPM sensors in :func:`mne.preprocessing.compute_proj_hfc` (:gh:`11536` by :newcontrib:`George O'Neill` and `Eric Larson`_)
• Forward argument axes from mne.viz.plot_sensors to mne.channels.DigMontage.plot (:gh:`11470` by :newcontrib:`Jan Ebert` and `Mathieu Scheltienne`_)
• Add forward IIR filtering, using parameters method='iir', phase='forward' (:gh:`11078` by :newcontrib:`Quentin Barthélemy`)
• Added ability to read stimulus durations from SNIRF files when using :func:`mne.io.read_raw_snirf` (:gh:`11397` by `Robert Luke`_)
• Add :meth:`mne.Info.save` to save an :class:`mne.Info` object to a fif file (:gh:`11401` by `Alex Rockhill`_)
• Improved error message when downloads are corrupted for :func:`mne.datasets.sample.data_path` and related functions (:gh:`11407` by `Eric Larson`_)
• Improved :func:`mne.get_config("") <mne.get_config>` behavior to return a dict of key-value pairs (config key and its description) rather than just a tuple of config keys (:gh:`11166` by `Clemens Brunner`_, `Daniel McCloy`_, and `Eric Larson`_)
• Add support for skip_by_annotation in :func:`mne.io.Raw.notch_filter` (:gh:`11388` by `Mainak Jas`_)
• Add support for output='complex' to :func:`mne.time_frequency.psd_array_welch` and when using method='welch' with :meth:`mne.Epochs.compute_psd` (:gh:`11556` by `Eric Larson`_)
• Slightly adjusted the window title for :func:`mne.Epochs.plot` (:gh:`11419` by `Richard Höchenberger`_ and `Daniel McCloy`_)
• Add :func:`mne.count_events` to count unique event types in a given event array (:gh:`11430` by `Clemens Brunner`_)
• Add a video to :ref:`tut-freesurfer-mne` of a brain inflating from the pial surface to aid in understanding the inflated brain (:gh:`11440` by `Alex Rockhill`_)
• Add automatic projection of sEEG contact onto the inflated surface for :meth:`mne.viz.Brain.add_sensors` (:gh:`11436` by `Alex Rockhill`_)
• Allow an image with intracranial electrode contacts (e.g. computed tomography) to be used without the freesurfer recon-all surfaces to locate contacts so that it doesn't have to be downsampled to freesurfer dimensions (for microelectrodes) and show an example :ref:`ex-ieeg-micro` with :func:`mne.transforms.apply_volume_registration_points` added to aid this transform (:gh:`11567` by `Alex Rockhill`_)
• Use new :meth:`dipy.align.imwarp.DiffeomorphicMap.transform_points` to transform a montage of intracranial contacts more efficiently (:gh:`11572` by `Alex Rockhill`_)
• Improve performance of raw data browsing with many annotations (:gh:`11614` by `Eric Larson`_)
• Add support for :func:`mne.preprocessing.maxwell_filter` with gradient-compensated CTF data, e.g., for tSSS-only mode (:gh:`10554` by `Eric Larson`_)
• Add support for eyetracking data using :func:`mne.io.read_raw_eyelink` (:gh:`11152` by `Dominik Welke`_ and `Scott Huberty`_)
• :func:`mne.channels.make_1020_channel_selections` gained a new parameter, return_ch_names, to allow for easy retrieval of EEG channel names corresponding to the left, right, and midline portions of the montage (:gh:`11632` by `Richard Höchenberger`_)
• Methods for setting the sensor types of channels (e.g., for raw data, :meth:`mne.io.Raw.set_channel_types`) gained a new parameter, on_unit_change, to control behavior (raise an exception, emit a warning, or do nothing) in case the measurement unit is adjusted automatically (:gh:`11668` by `Richard Höchenberger`_)
• :func:`mne.beamformer.trap_music` implements the TRAP-MUSIC localisation algorithm with the same signature as :func:`mne.beamformer.rap_music` (:gh:`11679` by `Théodore Papadopoulo`_)

Bugs

• Improving compatibility with Qt6 by removing the use of deprecated AA_UseHighDpiPixmaps attribute for this Qt version (:gh:`11662` by :newcontrib:`Florin Pop`)
• Fix :func:`mne.time_frequency.psd_array_multitaper` docstring where argument bandwidth incorrectly reported argument as half-bandwidth and gave wrong explanation of default value (:gh:`11479` by :newcontrib:`Tom Stone`)
• Fix bug where installation of a package depending on mne will error when done in an environment where setuptools is not present (:gh:`11454` by :newcontrib:`Arne Pelzer`)
• Fix bug in :meth:`mne.Annotations.rename` where replacements were not done correctly (:gh:`11666` by :newcontrib:`Timur Sokhin` and `Eric Larson`_)
• Fix :meth:`mne.time_frequency.Spectrum.to_data_frame`'s docstring to reflect the correct name for the appended frequencies column (:gh:`11457` by :newcontrib:`Zvi Baratz`)
• Fix bug with :func:`mne.io.read_raw_egi` where events outside the recording window could break data reading (:gh:`11505` by :newcontrib:`Niels Focke`)
• Fix bug where :func:`mne.preprocessing.regress_artifact` and :class:`mne.preprocessing.EOGRegression` incorrectly tracked picks (:gh:`11366` by `Eric Larson`_)
• Fix bug where channel names were not properly sanitized in :func:`mne.write_evokeds` and related functions (:gh:`11399` by `Eric Larson`_)
• Fix bug where splash screen would not always disappear (:gh:`11398` by `Eric Larson`_)
• Fix bug where having a different combination of volumes loaded into freeview caused different affines to be returned by :func:`mne.read_lta` for the same Linear Transform Array (LTA) (:gh:`11402` by `Alex Rockhill`_)
• Fix how :class:`mne.channels.DigMontage` is set when using mne.gui.locate_ieeg so that :func:`mne.Info.get_montage` works and does not return None (:gh:`11421` by `Alex Rockhill`_)
• Fix :func:`mne.io.read_raw_edf` when reading EDF data with different sampling rates and a mix of data channels when using infer_types=True (:gh:`11427` by `Alex Gramfort`_)
• Fix how :class:`mne.channels.DigMontage` is set when using :func:`mne.preprocessing.ieeg.project_sensors_onto_brain` so that :func:`mne.Info.get_montage` works and does not return None (:gh:`11436` by `Alex Rockhill`_)
• Fix configuration folder discovery on Windows, which would fail in certain edge cases; and produce a helpful error message if discovery still fails (:gh:`11441` by `Richard Höchenberger`_)
• Make :class:`~mne.decoding.SlidingEstimator` and :class:`~mne.decoding.GeneralizingEstimator` respect the verbose argument. Now with verbose=False, the progress bar is not shown during fitting, scoring, etc. (:gh:`11450` by `Mikołaj Magnuski`_)
• Fix bug with mne.gui.locate_ieeg where Freesurfer ?h.pial.T1 was not recognized and suppress excess logging (:gh:`11489` by `Alex Rockhill`_)
• All functions accepting paths can now correctly handle :class:`~pathlib.Path` as input. Historically, we expected strings (instead of "proper" path objects), and only added :class:`~pathlib.Path` support in a few select places, leading to inconsistent behavior. (:gh:`11473` and :gh:`11499` by `Mathieu Scheltienne`_)
• Fix visualization dialog compatibility with matplotlib 3.7 (:gh:`11409` by `Daniel McCloy`_ and `Eric Larson`_)
• Expand tilde (user directory) in config keys (:gh:`11537` by `Clemens Brunner`_)
• Fix bug in :func:`mne.preprocessing.compute_maxwell_basis` where using int_order=0 would raise an error (:gh:`11562` by `Eric Larson`_)
• In the legacy function :func:`mne.viz.plot_epochs_psd_topomap`, the parameter names now works again (:gh:`11563` by `Daniel McCloy`_)
• Fix :func:`mne.io.read_raw` for file names containing multiple dots (:gh:`11521` by `Clemens Brunner`_)
• Fix bug in :func:`mne.export.export_raw` when exporting to EDF with a physical range set smaller than the data range (:gh:`11569` by `Mathieu Scheltienne`_)
• Fix bug in :func:`mne.concatenate_raws` where two raws could not be merged if the order of the bad channel lists did not match (:gh:`11502` by `Moritz Gerster`_)
• Fix bug where :meth:`mne.Evoked.plot_topomap` opened an extra figure (:gh:`11607` by `Alex Rockhill`_)
• Fix bug where :func:`mne.transforms.apply_volume_registration_points` modified info in place (:gh:`11612` by `Alex Rockhill`_)
• Fix bug where Maxwell-filtered data rank was not handled properly in :func:`mne.beamformer.make_lcmv` (:gh:`11664` by `Eric Larson`_)
• In :class:`~mne.Report`, custom figures now show up correctly when image_format='svg' is requested (:gh:`11623` by `Richard Höchenberger`_)
• Fix bug where providing axes in mne.preprocessing.ICA.plot_components would fail (:gh:`11654` by `Mathieu Scheltienne`_)
• Fix deprecation of title, vmin and vmax in ~mne.viz.plot_tfr_topomap called from interactive mne.time_frequency.AverageTFR.plot_topo (:gh:`11683` by `Mathieu Scheltienne`_)

API changes

• Deprecate mne.gui.locate_ieeg in favor of :func:`mne-gui-addons:mne_gui_addons.locate_ieeg` (:gh:`11616` by `Alex Rockhill`_)
• Deprecate arguments kind and path from :func:`mne.channels.read_layout` in favor of a common argument fname (:gh:`11500` by `Mathieu Scheltienne`_)
• Change aligned_ct positional argument in mne.gui.locate_ieeg to base_image to reflect that this can now be used with unaligned images (:gh:`11567` by `Alex Rockhill`_)
• mne.warp_montage_volume was deprecated in favor of :func:`mne.preprocessing.ieeg.warp_montage` (acts directly on points instead of using an intermediate volume) and :func:`mne.preprocessing.ieeg.make_montage_volume` (which makes a volume of ieeg contact locations which can still be useful) (:gh:`11572` by `Alex Rockhill`_)
• Deprecate mne.pick_channels_evoked in favor of evoked.copy().pick(...) (:gh:`11665` by `Eric Larson`_)
• Set instance methods inst.pick_types and inst.pick_channels as legacy in favor of inst.pick(...) (:gh:`11665` by `Eric Larson`_)
• The default of inst.pick_channels(..., ordered=False) will change to ordered=True in 1.5 to avoid silent bugs (:gh:`11665` by `Eric Larson`_)

Authors

• Alex Rockhill
• Alexandre Gramfort
• Arne Pelzer+
• Britta Westner
• Carlos de la Torre
• Clemens Brunner
• Daniel Hasegan
• Daniel McCloy
• Denis A. Engemann
• Dimitri Papadopoulos Orfanos
• Dinara Issagaliyeva
• Dominik Welke
• Enzo Altamiranda
• Eric Brayet
• Eric Larson
• Erkka Heinila
• Felix Klotzsche
• Florin Pop+
• George O'Neill+
• Giulio
• Hakimeh Aslsardroud
• Hyonyoung Shin+
• Jacob Woessner+
• Jan Ebert+
• Jennifer Behnke
• Jevri Hanna
• Lukas Hecker
• Mainak Jas
• Mark Alexander Henney
• Mathieu Scheltienne
• Mauricio Cespedes
• Michiru Kaneda
• Mikołaj Magnuski
• Moritz Gerster
• Niels Focke+
• Omer Shubi
• Pavel Navratil
• Quentin Barthélemy+
• Richard Höchenberger
• Rob Luke
• Robert Seymour+
• Santeri Ruuskanen
• Sawradip Saha+
• Scott Huberty
• Stefan Appelhoff
• Theodore Papadopoulo
• Thomas Samuel Binns+
• Timon Merk
• Timur Sokhin+
• Tom Ma
• Tom Stone+
• Toomas Erik Anijärv
• Zvi Baratz+