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v1.6.x

v1.6.0 (2024-03-01)

🆕 New features & enhancements

  • Added regress_artifact to allow artifact regression (e.g., of MEG reference sensors in KIT systems) (#837 by @larsoner)
  • Chosen reject parameters are now saved in the generated HTML reports (#839 by @larsoner)
  • Added saving of clean raw data in addition to epochs (#840 by @larsoner)
  • Added saving of detected blink and cardiac events used to calculate SSP projectors (#840 by @larsoner)
  • Added noise_cov_method to allow for the use of methods other than "shrunk" for noise covariance estimation (#854 by @larsoner)
  • Added option to pass image_kwargs to [mne.Report.add_epochs] to allow adjusting e.g. "vmin" and "vmax" of the epochs image in the report via report_add_epochs_image_kwargs. This feature requires MNE-Python 1.7 or newer. (#848 by @SophieHerbst)
  • Split ICA fitting and artifact detection into separate steps. This means that now, ICA is split into a total of three consecutive steps: fitting, artifact detection, and the actual data cleaning step ("applying ICA"). This makes it easier to experiment with different settings for artifact detection without needing to re-fit ICA. (#865 by @larsoner)
  • The configuration used for the pipeline is now saved in a separate spreadsheet in the .xlsx log file (#869 by @larsoner)

📦 Requirements

🐛 Bug fixes

  • Fixed minor issues with path handling for cross-talk and calibration files (#834 by @larsoner)
  • Fixed EEG reject use for ch_types = ["meg", "eeg"] in epoch cleaning (#839 by @larsoner)
  • Fixed bug where implicit mf_reference_run could change across invocations of mne_bids_pipeline, breaking caching (#839 by @larsoner)
  • Fixed --no-cache behavior having no effect (#839 by @larsoner)
  • Fixed Maxwell filtering failures when find_noisy_channels_meg = False` is used (#847 by @larsoner)
  • Fixed raw, empty-room, and custom noise covariances calculation, previously they could errantly be calculated on data without ICA or SSP applied (#840 by @larsoner)
  • Fixed multiple channel type handling (e.g., MEG and EEG) in decoding (#853 by @larsoner)
  • Changed the default for ica_n_components from 0.8 (too conservative) to None to match MNE-Python's default (#853 by @larsoner)
  • Prevent events table for the average subject overflowing in reports (#854 by @larsoner)
  • Fixed split file behavior for Epochs when using ICA (#855 by @larsoner)
  • Fixed a bug where users could not set _components.tsv as it would be detected as a cache miss and overwritten on next pipeline run (#865 by @larsoner)

⚕ Code health

  • The package build backend has been switched from setuptools to hatchling. (#825 by @hoechenberger)
  • Removed dependencies on datalad and git-annex for testing (#867 by @larsoner)
  • Code formatting now uses ruff format instead of black (#834, #838 by @larsoner)
  • Code caching is now tested using GitHub Actions (#836 by @larsoner)
  • Steps in the documentation are now automatically parsed into flowcharts (#859 by @larsoner)
  • New configuration options are now automatically added to the docs (#863 by @larsoner)
  • Configuration options now have relevant steps listed in the docs (#866 by @larsoner)