Presets ======= .. seealso:: :ref:`tut-quickstart` runs the ``eeg-erp`` preset from raw data to epochs. Presets are ready-made pipelines. They are ordinary :class:`~meeg_utils.Pipeline` objects: change any parameter with ``set_params``, edit steps, or export them to YAML. .. code-block:: python import meeg_utils as meu meu.presets.available() pipe = meu.Pipeline.preset("had-meeg", datatype="meg") Recommended presets ------------------- ``eeg-erp``, ``eeg-rest``, ``meg-erp`` and ``meg-rest`` are the pipelines this library recommends. Every parameter comes from a published default (MNE-BIDS-Pipeline, the requirements of ICLabel and MEGnet, PREP, ZapLine-plus, autoreject, Tanner et al. 2015 for the high-pass); parameters without an accepted default must be given. The sources are listed step by step in `docs/presets/recommended.md `_. Each has two stages, applied per run: .. code-block:: python pre = meu.Pipeline.preset("meg-erp", system="neuromag") # or "ctf", "kit" clean = pre.fit_transform(run) ep = meu.Pipeline.preset("meg-erp", stage="epochs", event_id=["face", "house"], head_destination=meu.io.average_dev_head_t(runs)) epochs = ep.fit_transform(clean) # several runs: meu.epochs.combine([...]) - **preprocessing** -- EEG: bridged electrodes, 0.1 Hz high-pass, ZapLine-plus, PREP, interpolation, average reference, ICA with ICLabel. MEG: system-specific noise reduction (Neuromag: SSS; CTF: grade-3 gradiometers; KIT: reference regression), 0.1 Hz high-pass, ZapLine-plus, 250 Hz, 20-component ICA with MEGnet. - **epochs** -- ERP: 40 Hz low-pass, -0.2 to 0.5 s around ``event_id``, pre-stimulus baseline. Rest: consecutive windows of ``epoch_duration``. Both end with local autoreject. Dataset presets --------------- Dataset presets reproduce the preprocessing of a published dataset with its known problems fixed. Every difference from the original code is documented with its reason. ``had-meeg`` ------------ The per-run preprocessing of `HAD-MEEG `_ for CTF MEG (``datatype="meg"``) or EEG (``datatype="eeg"``): 0.1-100 Hz, 250 Hz, bad channels (Maxwell / PREP), interpolation, ZapLine-plus, CTF grade-3 compensation or average reference, and ICA labelled with MEGnet / ICLabel. The list of corrections, including those for the original epoching stage (head alignment, baseline, mastoid reference), is in `docs/presets/had-meeg.md `_.