osl_ephys.preprocessing.ica_label#

OSL ICA LABEL Tool for interactive ICA component labeling and rejection. Works with command line arguments or as a function call.

Attributes#

logger

Functions#

`ica_label`(data_dir, subject[, reject, interactive])	Data bookkeeping and wrapping plot_ica.
`main`([argv])	Command-line interface for ica_label.
`apply`([argv])	Command-line function for removing all labeled components from the data.

Module Contents#

osl_ephys.preprocessing.ica_label.logger = None[source]#

osl_ephys.preprocessing.ica_label.ica_label(data_dir, subject, reject=None, interactive=True)[source]#

Data bookkeeping and wrapping plot_ica.

Parameters:

data_dir (str) – Path to processed (M/EEG) data.
subject (str) – Subject/session specific data directory name
reject (bool or str) – If ‘all’, reject all components (previously labeled and newly labeled). If ‘manual’, reject only manually labeled components. If None (default), only save the ICA data; don’t reject any components from the M/EEG data.

osl_ephys.preprocessing.ica_label.main(argv=None)[source]#

Command-line interface for ica_label.

Parameters:: argv (list) – List of strings to be parsed as command-line arguments. If None, sys.argv will be used.

Example

From the command line (in the osl-ephys environment), use as follows:

osl_ica_label reject_argument /path/to/processed_data subject_name

The reject_argument specifies whether to reject ‘all’ selected components from the data, only the ‘manual’ rejected, or None (and only save the ICA object, without rejecting components). The subject_name should be the name of the subject directory in the processed data directory. The /path/to/processed_data can be omitted when the command is run from the processed data directory. If both the subject_name and directory are omitted, the script will attempt to process all subjects in the processed data directory. For example:

osl_ica_label manual /path/to/proc_dir sub-001_run01

or:

osl_ica_label all sub-001_run01

Then use the GUI to label components (click on the time course to mark, use number keys to label marked components as specific artefacts, and use the arrow keys to navigate. Close the plot. all/manual/None components will be removed from the M/EEG data and saved. The ICA data will be saved with the new labels. If the report directory is specified or in the assumed osl-ephys directory structure, the subject report and log file is updated.

osl_ephys.preprocessing.ica_label.apply(argv=None)[source]#

Command-line function for removing all labeled components from the data.

Parameters:: argv (list) – List of strings to be parsed as command-line arguments. If None, sys.argv will be used.

Example

From the command line (in the osl-ephys environment), use as follows:

osl_ica_apply /path/to/processed_data subject_name

The subject_name should be the name of the subject directory in the processed data directory. If omitted, the script will attempt to process all subjects in the processed data directory. The /path/to/processed_data can also be omitted when the command is run from the processed data directory (only when processing all subjects).

For example:

osl_ica_apply /path/to/proc_dir sub-001_run01

or:

osl_ica_apply

Then use the GUI to label components (click on the time course to mark, use number keys to label marked components as specific artefacts, and use the arrow keys to navigate. Close the plot. all/manual/None components will be removed from the M/EEG data and saved. The ICA data will be saved with the new labels. If the report/logs directories are in the assumed osl-ephys directory structure, the subject report and log file are updated.