What’s new?

Version 0.6 🎄

These are challenging days for many of us, and to make your lives ever so slightly easier, we’ve been working hard to deliver this early Christmas present 🎁 And even if you do not celebrate Christmas, we are quite certain you will like what we got for you! So – what are you waiting for? It’s time to unwrap!

Notable changes

• The new Inspector, which can be invoked via mne_bids.inspect_dataset(), allows you to interactively explore your raw data, change the bad channels selection, and edit mne.Annotations. It also performs automated detection of flat data segments or channels, to assist you during visual inspection. The capabilities of the inspector will be further expanded in upcoming releases of MNE-BIDS.

• To further assist you during data inspection, we have added a function to summarize all events present in a dataset, mne_bids.stats.count_events().

• Sidecar JSON files can now be updated using a template via mne_bids.update_sidecar_json().

• You can now read and write FLASH MRI images using mne_bids.write_anat(). We also fixed some issues with MRI defacing along the way.

• Event durations are now preserved upon reading and writing data (we used to set all event durations to zero before).

Authors

• Stefan Appelhoff

• Adam Li

• Alex Rockhill

• Alexandre Gramfort

• Austin Hurst

• Ethan Knights (new contributor)

• Mainak Jas

• Richard Höchenberger

Detailed list of changes

Enhancements

• The function mne_bids.print_dir_tree() has a new parameter return_str which allows it to return a str of the dir tree instead of printing it, by Stefan Appelhoff (#600)

• The function mne_bids.print_dir_tree() has a new parameter return_str which allows it to return a str of the dir tree instead of printing it, by Stefan Appelhoff (#600)

• mne_bids.write_raw_bids() now preserves event durations when writing mne.Annotations to *_events.tsv files, and mne_bids.read_raw_bids() restores these durations upon reading, by Richard Höchenberger (#603)

• Writing BrainVision data via mne_bids.write_raw_bids() will now set the unit of EEG channels to µV for enhanced interoperability with other software, by Alexandre Gramfort, Stefan Appelhoff, and Richard Höchenberger (#610)

• New function mne_bids.stats.count_events() to easily summarize all the events present in a dataset, by Alexandre Gramfort (#629)

• Add mne_bids.update_sidecar_json() to allow updating sidecar JSON files with a template, by Adam Li and Austin Hurst (#601)

• Add support for anonymizing EDF and BDF files without converting to BrainVision format, by Austin Hurst (#636)

• Add support for writing FLASH MRI data with mne_bids.write_anat(), by Alexandre Gramfort (#641)

• Add interactive data inspector mne_bids.inspect_dataset(), by Richard Höchenberger (#561)

• Do not complain about missing events if it’s likely we’re dealing with resting-state data in mne_bids.write_raw_bids(), by new contributor Ethan Knights (#631)

API changes

• When passing event IDs to mne_bids.write_raw_bids() via events_data without an accompanying event description in event_id, we will now raise a ValueError. This ensures that accidentally un-described events won’t get written unnoticed, by Richard Höchenberger (#603)

• The mne_bids.get_head_mri_trans() now has a parameter extra_params to allow passing arguments specific to a file format, by Mainak Jas (#638)

• The first parameter of mne_bids.write_anat() is now called image and not t1w, by Alexandre Gramfort (#641)

Requirements

• Writing BrainVision data now requires pybv 0.4 or later.

Bug fixes

• Make sure large FIF files with splits are handled transparently on read and write, by Alexandre Gramfort (#612)

• The function mne_bids.write_raw_bids() now outputs *_electrodes.tsv and *_coordsystem.json files for EEG/iEEG data that are BIDS-compliant (only contain subject, session, acquisition, and space entities), by Adam Li (#601)

• Make sure writing empty-room data with anonymization shifts the session back in time, by Alexandre Gramfort (#611)

• Fix a bug in mne_bids.write_raw_bids(), where passing raw data with mne.Annotations set and the event_id dictionary not containing the mne.Annotations descriptions as keys would raise an error, by Richard Höchenberger (#603)

• Fix a bug in mne_bids.write_raw_bids() when passing raw MEG data with Internal Active Shielding (IAS) from Triux system, by Alexandre Gramfort (#616)

• Fix a bug in mne_bids.write_raw_bids(), where original format of data was not kept when writing to FIFF, by Alexandre Gramfort, Stefan Appelhoff, and Richard Höchenberger (#610)

• Fix a bug where conversion to BrainVision format was done even when non-Volt channel types were present in the data (BrainVision conversion is done by pybv, which currently only supports Volt channel types), by Stefan Appelhoff (#619)

• Ensure sidecar files (tsv and json) are always read and written in UTF-8, by Richard Höchenberger (#625)

• Fix a bug where participants.tsv was not being appended to correctly when it contained a subset of hand, age and sex, by Adam Li (#648)

• mne_bids.copyfiles.copyfile_eeglab() didn’t handle certain EEGLAB files correctly, by Richard Höchenberger (#653)

• Fix bug where images with different orientations than the T1 used to define the landmarks were defaced improperly, by Alex Rockhill (#651)

Find out what was new in previous releases