What’s new?

Version 0.7

This release brings numerous enhancements and bug fixes that enhance reading and writing BIDS data, and improve compatibility with the latest BIDS specifications.

Notable changes

• Channel names in *_channels.tsv and *_electrodes.tsv files now always take precedence over the names stored in the raw files.

• When reading data where the same trial type refers to different trigger values, we will now automatically create hierarchical event names in the form of trial_type/value1, trial_type/value2` etc.

• mne_bids.write_raw_bids() now allows users to specify a format conversion via the new format parameter.

• Various improvements to data reading and mne_bids.BIDSPath make working with real-life data easier.

• Many bug fixes in mne_bids.write_raw_bids() and in the MNE-BIDS Inspector.

Authors

• Adam Li

• Alexandre Gramfort

• Austin Hurst

• Diego Lozano-Soldevilla

• Eduard Ort

• Maximilien Chaumon

• Richard Höchenberger

• Stefan Appelhoff

• Tom Donoghue

Detailed list of changes

Enhancements

• Some datasets out in the real world have a non-standard stim_type instead of a trial_type column in *_events.tsv. mne_bids.read_raw_bids() now makes use of this column, and emits a warning, encouraging users to rename it, by Richard Höchenberger (#680)

• When reading data where the same event name or trial type refers to different event or trigger values, we will now create a hierarchical event name in the form of trial_type/value, e.g. stimulus/110, by Richard Höchenberger (#688)

• When reading data via mne_bids.read_raw_bids(), the channel names specified in the BIDS *_channels.tsv and *_electrodes.tsv files now always take precedence over (and do not need to match) the channel names stored in the raw files anymore, by Adam Li and Richard Höchenberger (#691, #704)

• Improve the Convert iEEG data to BIDS tutorial to include a note on how BIDS and MNE-Python coordinate frames are handled, by Adam Li (#717)

• More detailed error messages when trying to write modified data via mne_bids.write_raw_bids(), by Richard Höchenberger (#719)

• If check=True, mne_bids.BIDSPath now checks the space entity to be valid according to BIDS specification Appendix VIII, by Stefan Appelhoff (#724)

• Data types that are currently unsupported by MNE-BIDS (e.g. dwi, func) can now be used in mne_bids.BIDSPath by setting check=False, by Adam Li (#744)

• Arbitrary file names can now be represented as a BIDSPath` by passing the entire name as suffix and setting check=False, by Adam Li (#729)

• Add support for MNE’s flux excitation channel (exci), by Maximilien Chaumon (#728)

• mne_bids.BIDSPath.match() gained a new parameter check; when setting check=True, match() will only return paths that conform to BIDS, by Richard Höchenberger (#726)

• BIDSPath.root now automatically expands ~ to the user’s home directory, by Richard Höchenberger (#725)

API and behavior changes

• Add format kwarg to mne_bids.write_raw_bids() that allows users to specify if they want to force conversion to BrainVision or FIF file format, by Adam Li (#672)

• mne_bids.read_raw_bids() now stores the participant_id value from participants.tsv in raw.info['subject_info']['his_id'], not in raw.info['subject_info']['participant_id'] anymore, by Richard Höchenberger (#745)

Requirements

• For writing BrainVision files, pybv version 0.5 is now required to allow writing of non-voltage channels, by Adam Li (#670)

Bug fixes

• Fix writing MEGIN Triux files, by Alexandre Gramfort (#674)

• Anonymization of EDF files in write_raw_bids() will now convert recording date to 01-01-1985 00:00:00 if anonymization takes place, while setting the recording date in the scans.tsv file to the anonymized date, thus making the file EDF/EDFBrowser compliant, by Adam Li (#669)

• mne_bids.write_raw_bids() will not overwrite an existing coordsystem.json anymore, unless explicitly requested, by Adam Li (#675)

• mne_bids.read_raw_bids() now properly handles datasets without event descriptions, by Richard Höchenberger (#680)

• mne_bids.stats.count_events() now handles files without a trial_type or stim_type column gracefully, by Richard Höchenberger (#682)

• mne_bids.read_raw_bids() now correctly treats coordsystem.json as optional for EEG and MEG data, by Diego Lozano-Soldevilla (#691)

• mne_bids.read_raw_bids() now ignores exclude parameters passed via extra_params, by Richard Höchenberger (#703)

• mne_bids.write_raw_bids() now retains original event IDs in the value column of *_events.tsv, by Richard Höchenberger (#708)

• Fix writing correct iEEGCoordinateSystemDescription, by Stefan Appelhoff (#706)

• FIF files that were split due to filesize limitations (using the _split-<label> entity), are now all listed in scans.tsv, as recommended by BIDS, by Eduard Ort (#710)

• The mne_bids inspect command now automatically tries to discover flat channels by default; this should have been the case all along, but the default parameter was set incorrectly, by Richard Höchenberger (#726)

• mne_bids.inspect_dataset() would sometimes open the same file multiple times, by Richard Höchenberger (#726)

• mne_bids.inspect_dataset() would try to open the SSP projector selection window for non-MEG data, by Richard Höchenberger (#726)

Find out what was new in previous releases