List of processing steps

The following table provides a concise summary of each processing step. The step names can be used to run individual steps or entire groups of steps by passing their name(s) to mne_bids_pipeline via the steps=... argument. However, we recommend using mne_bids_pipeline config.py to run the entire pipeline instead to ensure that all steps affected by a given change are re-run.

1. Filesystem initialization and dataset inspection

Step name	Description
init	Run all filesystem initialization and dataset inspection steps.
init/_01_init_derivatives_dir	Initialize derivatives_dir.
init/_02_find_empty_room	Find empty-room data matches.

2. Preprocessing

Step name	Description
preprocessing	Run all preprocessing steps.
preprocessing/_01_data_quality	Assess data quality and find bad (and flat) channels.
preprocessing/_02_head_pos	Estimate head positions.
preprocessing/_03_maxfilter	Maxwell-filter MEG data.
preprocessing/_04_frequency_filter	Apply low- and high-pass filters.
preprocessing/_05_regress_artifact	Temporal regression for artifact removal.
preprocessing/_06a1_fit_ica	Fit ICA.
preprocessing/_06a2_find_ica_artifacts	Find ICA artifacts.
preprocessing/_06b_run_ssp	Compute SSP.
preprocessing/_07_make_epochs	Extract epochs.
preprocessing/_08a_apply_ica	Apply ICA.
preprocessing/_08b_apply_ssp	Apply SSP.
preprocessing/_09_ptp_reject	Remove epochs based on PTP amplitudes.

3. Sensor-space analysis

Step name	Description
sensor	Run all sensor-space analysis steps.
sensor/_01_make_evoked	Extract evoked data for each condition.
sensor/_02_decoding_full_epochs	Decode pairs of conditions based on entire epochs.
sensor/_03_decoding_time_by_time	Decode time-by-time using a "sliding" estimator.
sensor/_04_time_frequency	Time-frequency decomposition.
sensor/_05_decoding_csp	Decoding based on common spatial patterns (CSP).
sensor/_06_make_cov	Noise covariance estimation.
sensor/_99_group_average	Group average at the sensor level.

4. Source-space analysis

Step name	Description
source	Run all source-space analysis steps.
source/_01_make_bem_surfaces	Create BEM surfaces.
source/_02_make_bem_solution	Compute BEM solution.
source/_03_setup_source_space	Setup source space.
source/_04_make_forward	Forward solution.
source/_05_make_inverse	Inverse solution.
source/_99_group_average	Group average at the source level.

5. FreeSurfer-related processing

Surface reconstruction via FreeSurfer. These steps are not run by default.

Step name	Description
freesurfer	Run all freesurfer-related processing steps.
freesurfer/_01_recon_all	Run FreeSurfer's recon-all.
freesurfer/_02_coreg_surfaces	Generate coregistration surfaces.