Configuration Reference

Pipelines are defined in YAML. The top-level key is pipeline, which is a list of step objects. Each step has a name field plus any parameters that step accepts.

Minimal example

pipeline:
  - name: bandpass_filter
    l_freq: 0.5
    h_freq: 40.0
  - name: epoch
    tmin: -0.2
    tmax: 0.8
  - name: save_clean_instance

Available steps

Data loading / setup

Step	Key parameters
set_montage	montage (str), match_case (bool)
drop_unused_channels	channels (list)
strip_recording	tmin, tmax
copy_instance	source, dest
concatenate_recordings	instances (list)

Filtering

Step	Key parameters
bandpass_filter	l_freq, h_freq, picks, n_jobs
notch_filter	freqs (list), picks, n_jobs
resample	sfreq, npad, n_jobs, resample_events

Referencing

Step	Key parameters
reference	ref_channels (default 'average'), instance

Bad channel detection

Step	Key parameters
find_flat_channels	threshold (default 1e-12), picks, excluded_channels
find_bads_channels_threshold	reject (dict), n_epochs_bad_ch, picks, apply_on
find_bads_channels_variance	zscore_thresh, max_iter, picks, instance, apply_on
find_bads_channels_high_frequency	zscore_thresh, max_iter, picks, instance, apply_on

Bad channel handling

Step	Key parameters
interpolate_bad_channels	instance, picks
drop_bad_channels	instance

ICA

Step	Key parameters
ica	n_components, method, fit_params, picks, eog_channel, ecg_channel

Epoching

Step	Key parameters
find_events	get_events_from ('annotations'|'stim_channel'), shortest_event, event_id, stim_channel
epoch	event_id, tmin, tmax, baseline, reject
chunk_in_epoch	duration
find_bads_epochs_threshold	reject (dict), n_channels_bad_epoch, picks

Output

Step	Key parameters
save_clean_instance	instance ('raw'|'epochs'), overwrite
generate_json_report	(no parameters)
generate_html_report	picks, excluded_channels, outlines, compare_instances

Common parameter patterns

picks

Accepts any value that MNE's pick_types understands (e.g. 'eeg', ['eeg', 'meg'], or a list of channel names).

excluded_channels

A list of channel names to exclude from the step (e.g. reference electrodes).

apply_on

Some bad-channel detection steps accept apply_on: [raw, epochs] to mark the found bad channels on multiple instances simultaneously.

instance

Steps that can act on either raw or epoched data accept an instance key: 'raw' or 'epochs'.