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. |
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. |