Using these plugins from the command line¶
The three plugins take the same parameters — only the --run name and, for EEG/sEEG, the extra PSD
band parameters, differ. None of them currently support --use_markers/--skip_markers to restrict
the analyzed portion of the file: the whole recording is always analyzed.
| option | type | description/value |
|---|---|---|
| --run "MEG Artifact Detector" / "EEG Artifact Detector" / "SEEG Artifact Detector" | MANDATORY | name of the plugin (quote it — the name contains spaces) |
| --window_length_s value | optional (default 5.0) | analysis window length, in seconds |
| --zscore_threshold value | optional (default 5.0) | robust z-score threshold for criteria 1/2/5 |
| --global_bad_ratio value | optional (default 0.8) | fraction of flagged windows above which a channel is treated as persistently bad |
| --neighbor_count value | optional (default 5, sEEG: 2) | number of neighbors used by criteria 2/3 |
| --psd_pair_zscore_threshold value | optional (default 3.0) | robust z-score threshold, criterion 3 |
| --psd_peak_zscore_threshold value | optional (default 3.0) | robust z-score threshold, criterion 4 |
| --psd_band_low_hz / --psd_band_high_hz value | optional, EEG/sEEG only (default 20/70) | criterion 3 broadband range, in Hz |
| --psd_peak_low_hz / --psd_peak_high_hz value | optional, EEG/sEEG only (default 2/100) | criterion 4 peak-search range, in Hz |
See the shared methodology page for what each parameter actually controls.
This plugin also supports the following common options:
| option | type |
|---|---|
| --input_file | MANDATORY |
| --output_dir | optional |
| --output_file | optional |
--skip_bad_channels does not apply here
A plain --run invocation builds its channel list from the file's default montage, which
already excludes any channel listed in its .bad sidecar, regardless of --skip_bad_channels
(that option only affects a few other command-line code paths, not a plain --run). To review
channels that are already marked bad, run against a copy of the file without its .bad
sidecar.
Output¶
Each run writes one .mrk file to --output_dir (defaults to the input file's own directory)
containing the transient (criterion 5) markers, labeled "artifact". Channels flagged by any
criterion are colored red directly in the montage when run from the GUI; from the command line
there is no view to color, so check the log for the list of flagged channels instead.
Default output file name, if --output_file isn't given: <input file base name>_megartifact.mrk
/ _eegartifact.mrk / _seegartifact.mrk.
Examples¶
MEG, default parameters¶
anywave --run "MEG Artifact Detector" --input_file d:\data\myfile.meg4
EEG, custom analysis window and threshold¶
anywave --run "EEG Artifact Detector" --input_file d:\data\myfile.edf --window_length_s 4 --zscore_threshold 4.5
sEEG, custom output location¶
anywave --run "SEEG Artifact Detector" --input_file d:\data\myfile.trc --output_dir d:\results --output_file myfile_seeg_review.mrk