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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. ๐Ÿ“‚ 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. ๐Ÿงน 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. ๐Ÿ“ก 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. ๐Ÿง  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.

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.