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mne_bids

What's new?

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! 🤩

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

Detailed list of changes

🚀 Enhancements

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

🧐 API and behavior changes

  • ~mne_bids.write_raw_bids now expects all but the first four parameters to be passed as keyword arguments, by Richard Höchenberger (1054)
  • The events_data parameter of ~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 (1054)
  • In many places, we used to infer the datatype of a ~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 (1030)
  • 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 (406)
  • The deprecated function mne_bids.mark_bad_channels has been removed in favor of mne_bids.mark_channels, by Richard Höchenberger (1009)
  • mne_bids.print_dir_tree now raises a :pyFileNotFoundError instead of a :pyValueError if the directory does not exist, by Richard Höchenberger (1013)
  • Passing only one of events and event_id to ~mne_bids.write_raw_bids now raises a ValueError instead of a RuntimeError, by Richard Höchenberger (1054)
  • Until now, 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 (1061)
  • Provide a more helpful error message when trying to write non-preloaded concatenated data, by Richard Höchenberger (#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 (1011)

🪲 Bug fixes

  • Fix ACPC in surface RAS instead of scanner RAS in ieeg-example and add convenience functions mne_bids.convert_montage_to_ras and mne_bids.convert_montage_to_mri to help, by Alex Rockhill (990)
  • Suppress superfluous warnings about MaxShield in many functions when handling Elekta/Neuromag/MEGIN data, by Richard Höchenberger (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 (1007)
  • ~mne_bids.copyfiles.copyfile_brainvision can now deal with .dat file extension, by Dominik Welke (1008)
  • ~mne_bids.print_dir_tree now correctly expands ~ to the user's home directory, by Richard Höchenberger (1013)
  • ~mne_bids.write_raw_bids now correctly excludes stim channels when writing to electrodes.tsv, by Scott Huberty (1023)
  • ~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 (1031)
  • Writing EEGLAB files was sometimes broken when .set and .fdt pairs were supplied. This is now fixed in ~mne_bids.copyfiles.copyfile_eeglab, by Stefan Appelhoff (1039)
  • Writing and copying CTF files now works on Windows when files already exist (overwrite=True), by Stefan Appelhoff (1035)
  • Instead of deleting files and raising cryptic errors, an intentional error message is now sent when calling ~mne_bids.write_raw_bids with the source file identical to the destination file, unless format is specified, by Adam Li and Stefan Appelhoff (889)
  • Internal helper function to ~mne_bids.read_raw_bids would reject BrainVision data if _scans.tsv listed a .eeg file instead of .vhdr, by Teon Brooks (1034)
  • Whenever ~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 (1052)
  • Fix the incorrect setting of the fields ContinuousHeadLocalization and HeadCoilFrequency for Neuromag MEG recordings, by Eduard Ort (1067)

Find out what was new in previous releases <whats_new_previous_releases>