What’s new?

Version 0.9 (2021-11-23)

This release brings compatibility with MNE-Python 0.24 and some new convenience functions and speedups of existing code to help you be more productive! 👩🏽‍💻 And, of course, plenty of bug fixes. 🐞

Notable changes

• 🧠 Compatibility with MNE-Python 0.24!

• 👻 Anonymize an entire BIDS dataset via mne_bids.anonymize_dataset()!

• 🏝 Conveniently turn a path into a BIDSPath via get_bids_path_from_fname()!

• 🏎 mne_bids.stats.count_events() and mne_bids.BIDSPath.match() are operating much faster now!

• 🔍 write_raw_bids() now stores the names of the input files in the source column of *_scans.tsv, making it easier for you to go back to the source should you ever need to!

Authors

People who contributed to this release (in alphabetical order):

• Adam Li

• Alex Rockhill

• Alexandre Gramfort

• Clemens Brunner

• Franziska von Albedyll

• Julia Guiomar Niso Galán

• Mainak Jas

• Marijn van Vliet

• Richard Höchenberger

• Stefan Appelhoff

Detailed list of changes

Enhancements

• mne_bids.get_anat_landmarks() now accepts a mne_bids.BIDSPath as image parameter, by Alex Rockhill (#852)

• mne_bids.write_raw_bids() now accepts 'EDF' as a 'format' value to force conversion to EDF files, by Adam Li (#866)

• mne_bids.write_raw_bids() now adds SpatialCompensation information to the JSON sidecar for MEG data, by Julia Guiomar Niso Galán (#885)

• Modify iEEG tutorial to use MNE raw object, by Alex Rockhill (#859)

• Add mne_bids.search_folder_for_text() to find specific metadata entries (e.g. all "n/a" sidecar data fields, or to check that “60 Hz” was written properly as the power line frequency), by Alex Rockhill (:gh: 870)

• Add mne_bids.get_bids_path_from_fname() to return a mne_bids.BIDSPath from a file path, by Adam Li (#883)

• Great performance improvements in mne_bids.stats.count_events() and mne_bids.BIDSPath.match(), significantly reducing processing time, by Richard Höchenberger (#888)

• The command mne_bids count_events gained new parameters: --output to direct the output into a CSV file; --overwrite to overwrite an existing file; and --silent to suppress output of the event counts to the console, by Richard Höchenberger (#888)

• The new function mne_bids.anonymize_dataset() can be used to anonymize an entire BIDS dataset, by Richard Höchenberger (#893, #914, #917)

• mne_bids.BIDSPath.find_empty_room() gained a new parameter use_sidecar_only to limit empty-room search to the metadata stored in the sidecar files, by Richard Höchenberger (#893)

• mne_bids.BIDSPath.find_empty_room() gained a new parameter verbose to limit verbosity of the output, by Richard Höchenberger (#893)

• mne_bids.write_raw_bids() can now write the source filename to scans.tsv in a new column, source, by Adam Li (#890)

API and behavior changes

• mne_bids.mark_bad_channels deprecated in favor of mne_bids.mark_channels(), which allows specifying the status to change channels to by Adam Li (#882)

• mne_bids.get_entities_from_fname() does not return suffix anymore as that is not considered a BIDS entity, by Adam Li (#883)

• Reading BIDS data with "HeadCoilFrequency" and "PowerLineFrequency" data specified in JSON sidecars will only “warn” in case of mismatches between Raw and JSON data, by Franziska von Albedyll (#855)

• Accessing mne_bids.BIDSPath.fpath emit a warning anymore if the path does not exist. This behavior was unreliable and yielded confusing error messages in certain use cases. Use mne_bids.BIDSPath.fpath.exists() to check whether the path exists in the file system, by Richard Höchenberger (#904)

• mne_bids.get_entity_vals() gained a new parameter, ignore_dirs, to exclude directories from the search, by Adam Li and Richard Höchenberger (#899, #908)

• In mne_bids.write_anat(), the deprecated parameters raw, trans, and t1w have been removed, by Richard Höchenberger (#909)

• In mne_bids.write_raw_bids(), any EDF output is always stored with lower-case extension (.edf), by Adam Li (#906)

Requirements

• MNE-BIDS now requires MNE-Python 0.24 or newer.

• Writing BrainVision files now requires pybv version 0.6, by Stefan Appelhoff (#880)

Bug fixes

• Fix writing Ricoh/KIT data that comes without an associated .mrk, .elp, or .hsp file using mne_bids.write_raw_bids(), by Richard Höchenberger (#850)

• Properly support CTF MEG data with 2nd-order gradient compensation, by Mainak Jas (#858)

• Fix writing and reading EDF files with upper-case extension (.EDF), by Adam Li (#868)

• Fix reading of TSV files with only a single column, by Marijn van Vliet (#886)

• Fix erroneous measurement date check in mne_bids.write_raw_bids() when requesting to anonymize empty-room data, by Richard Höchenberger (#893)

• mne_bids.write_raw_bids() now raises an exception if the provided mne_bids.BIDSPath doesn’t contain subject and task entities, which are required for neurophysiological data, by Richard Höchenberger (#903)

• mne_bids.read_raw_bids() now handles datasets with multiple electrophysiological data types correctly, by Richard Höchenberger (#910, :gh`916`)

• More robust handling of situations where mne_bids.read_raw_bids() tries to read a file that does not exist, by Richard Höchenberger (#904)

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