whats_new.rst

orphan:

.. currentmodule:: mne_bids

What's new?

Version 0.11.1 (2022-10-21)

Version 0.11.1 is a patch release, all changes are listed below. For more complete information on the 0.11 version, see changelog below.

• Speed up :func:`mne_bids.read_raw_bids` when lots of events are present by `Alexandre Gramfort`_ (:gh:`1079`)
• When writing data containing :class:`mne.Annotations` and passing events to :func:`~mne_bids.write_raw_bids`, previously, annotations whose description did not appear in event_id were silently dropped. We now raise an exception and request users to specify mappings between descriptions and event codes in this case. It is still possible to omit event_id if no events are passed, by `Richard Höchenberger`_ (:gh:`1084`)

Version 0.11 (2022-10-08)

This release includes a number of bug fixes as well as several smaller enhancements. Please note some behavior changes and updated requirements, as listed in the details below.

📝 Notable changes

• Support for new channel types is available: temperature and galvanic skin response
• MNE-BIDS now supports the BIDS "description" entity (desc)
• It's now possible to store Curry (CDT) files and EGI files with MNE-BIDS.

👩🏽‍💻 Authors

The following authors contributed for the first time. Thank you so much! 🤩

• `Anand Saini`_
• `Bruno Hebling Vieira`_
• `Daniel McCloy`_
• `Denis Engemann`_
• `Mathieu Scheltienne`_
• `Scott Huberty`_

The following authors had contributed before. Thank you for sticking around! 🤘

• `Adam Li`_
• `Alex Rockhill`_
• `Alexandre Gramfort`_
• `Dominik Welke`_
• `Eduard Ort`_
• `Eric Larson`_
• `Richard Höchenberger`_
• `Robert Luke`_
• `Stefan Appelhoff`_
• `Teon Brooks`_

Detailed list of changes

🚀 Enhancements

• You can now write raw data and an associated empty-room recording with just a single call to :func:`mne_bids.write_raw_bids`: the empty_room parameter now also accepts an :class:`mne.io.Raw` data object. The empty-room session name will be derived from the recording date automatically, by `Richard Höchenberger`_ (:gh:`998`)
• :func:`~mne_bids.write_raw_bids` now stores participant weight and height in participants.tsv, by `Richard Höchenberger`_ (:gh:`1031`)
• :func:`~mne_bids.write_raw_bids` now supports EGI format, by `Anand Saini`_, `Scott Huberty`_ and `Mathieu Scheltienne`_ (:gh:`1006`)
• When a given subject cannot be found, valid suggestions are now printed, by `Eric Larson`_ (:gh:`1066`)
• TSV files that are empty (i.e., only a header row is present) are now handled more robustly and a warning is issued, by `Stefan Appelhoff`_ (:gh:`1038`)
• :class:`~mne_bids.BIDSPath` now supports the BIDS "description" entity desc, used in derivative data, by `Richard Höchenberger`_ (:gh:`1049`)
• Added support for GSR (galvanic skin response / electrodermal activity, EDA) and TEMP (temperature) channel types, by `Richard Höchenberger`_ (:gh:`1059`)
• Added support for reading EEG files in Curry 8 format ('.cdt' extension) by `Denis Engemann`_ (:gh:`1072`)

🧐 API and behavior changes

• :func:`~mne_bids.write_raw_bids` now expects all but the first four parameters to be passed as keyword arguments, by `Richard Höchenberger`_ (:gh:`1054`)
• The events_data parameter of :func:`~mne_bids.write_raw_bids` has been deprecated in favor of a new parameter named events. This ensures more consistency between the MNE-BIDS and MNE-Python APIs. You may continue using the events_data parameter for now, but a FutureWarning will be raised. events_data will be removed in MNE-BIDS 0.14, by `Richard Höchenberger`_ (:gh:`1054`)
• In many places, we used to infer the datatype of a :class:`~mne_bids.BIDSPath` from the suffix, if not explicitly provided. However, this has lead to trouble in certain edge cases. In an effort to reduce the amount of implicit behavior in MNE-BIDS, we now require users to explicitly specify a datatype whenever the invoked functions or methods expect one, by `Richard Höchenberger`_ (:gh:`1030`)
• :func:`mne_bids.make_dataset_description` now accepts keyword arguments only, and can now also write the following metadata: HEDVersion, EthicsApprovals, GeneratedBy, and SourceDatasets, by `Stefan Appelhoff`_ (:gh:`406`)
• The deprecated function mne_bids.mark_bad_channels has been removed in favor of :func:`mne_bids.mark_channels`, by `Richard Höchenberger`_ (:gh:`1009`)
• :func:`mne_bids.print_dir_tree` now raises a :py:class:`FileNotFoundError` instead of a :py:class:`ValueError` if the directory does not exist, by `Richard Höchenberger`_ (:gh:`1013`)
• Passing only one of events and event_id to :func:`~mne_bids.write_raw_bids` now raises a ValueError instead of a RuntimeError, by `Richard Höchenberger`_ (:gh:`1054`)
• Until now, :class:`mne_bids.BIDSPath` prepends extensions with a period "." automatically. We intend to remove this undocumented side-effect and now emit a FutureWarning if an extension that does not start with a . is provided. Starting with MNE-BIDS 0.12, an exception will be raised in this case, by `Richard Höchenberger`_ (:gh:`1061`)
• Provide a more helpful error message when trying to write non-preloaded concatenated data, by `Richard Höchenberger`_ (:gh:`#1075`)

🛠 Requirements

• MNE-BIDS now requires MNE-Python 1.0 or newer.
• Writing BrainVision files now requires pybv version 0.7.3, by `Stefan Appelhoff`_ (:gh:`1011`)

🪲 Bug fixes

• Fix ACPC in surface RAS instead of scanner RAS in :ref:`ieeg-example` and add convenience functions :func:`mne_bids.convert_montage_to_ras` and :func:`mne_bids.convert_montage_to_mri` to help, by `Alex Rockhill`_ (:gh:`990`)
• Suppress superfluous warnings about MaxShield in many functions when handling Elekta/Neuromag/MEGIN data, by `Richard Höchenberger`_ (:gh:`1000`)
• The MNE-BIDS Inspector didn't work if mne-qt-browser was installed and used as the default plotting backend, as the Inspector currently only supports the Matplotlib backend, by `Richard Höchenberger`_ (:gh:`1007`)
• :func:`~mne_bids.copyfiles.copyfile_brainvision` can now deal with .dat file extension, by `Dominik Welke`_ (:gh:`1008`)
• :func:`~mne_bids.print_dir_tree` now correctly expands ~ to the user's home directory, by `Richard Höchenberger`_ (:gh:`1013`)
• :func:`~mne_bids.write_raw_bids` now correctly excludes stim channels when writing to electrodes.tsv, by `Scott Huberty`_ (:gh:`1023`)
• :func:`~mne_bids.read_raw_bids` doesn't populate raw.info['subject_info'] with invalid values anymore, preventing users from writing the data to disk again, by `Richard Höchenberger`_ (:gh:`1031`)
• Writing EEGLAB files was sometimes broken when .set and .fdt pairs were supplied. This is now fixed in :func:`~mne_bids.copyfiles.copyfile_eeglab`, by `Stefan Appelhoff`_ (:gh:`1039`)
• Writing and copying CTF files now works on Windows when files already exist (overwrite=True), by `Stefan Appelhoff`_ (:gh:`1035`)
• Instead of deleting files and raising cryptic errors, an intentional error message is now sent when calling :func:`~mne_bids.write_raw_bids` with the source file identical to the destination file, unless format is specified, by `Adam Li`_ and `Stefan Appelhoff`_ (:gh:`889`)
• Internal helper function to :func:`~mne_bids.read_raw_bids` would reject BrainVision data if _scans.tsv listed a .eeg file instead of .vhdr, by `Teon Brooks`_ (:gh:`1034`)
• Whenever :func:`~mne_bids.read_raw_bids` encounters a channel type that currently doesn't translate into an appropriate MNE channel type, the channel type will now be set to 'misc. Previously, seemingly arbitrary channel types would be applied, e.g. 'eeg' for GSR and temperature channels, by `Richard Höchenberger`_ (:gh:`1052`)
• Fix the incorrect setting of the fields ContinuousHeadLocalization and HeadCoilFrequency for Neuromag MEG recordings, by `Eduard Ort`_ (:gh:`1067`)

:doc:`Find out what was new in previous releases <whats_new_previous_releases>`