cmp.cli.visualize_eeg_pipeline_outputs module

This module defines the visualize_eeg_pipeline_outputs script that loads and displays the different MNE outputs of the EEG pipeline.

Examples

Here are a few usage examples:

1. Show all electrode epochs

   $ python cmp/cli/visualize_eeg_pipeline_outputs.py                 --epo_file /path/to/sub-01/eeg/sub-01_task-faces_epo.fif
   

2. Carpet plot of ROI time series when using Cartool for ESI

   $ python cmp/cli/visualize_eeg_pipeline_outputs.py                 --epo_file /path/to/sub-01/eeg/sub-01_task-faces_epo.fif                 --rtc_file /path/to/sub-01_task-faces_atlas-L2018_res-scale1_timeseries.npy                 --atlas_annot lausanne2018.scale1                 --fs_subject sub-01                 --fs_subjects_dir /path/to/derivatives/freesurfer-7.1.1                 --roi_tsv_file /path/to/sub-01_atlas-L2018_res-scale1_dseg.tsv
   

3. Carpet plot of ROI time series when using MNE for ESI

   $ python cmp/cli/visualize_eeg_pipeline_outputs.py                 --epo_file /path/to/sub-01/eeg/sub-01_task-faces_epo.fif                 --rtc_file /path/to/sub-01_task-faces_atlas-L2018_res-scale1_timeseries.npy                 --atlas_annot lausanne2018.scale1                 --fs_subject sub-01                 --fs_subjects_dir /path/to/derivatives/freesurfer-7.1.1                 --roi_tsv_file /path/to/sub-01_atlas-L2018_res-scale1_dseg.tsv
   

4. Display BEM surfaces only on T1w

   $ python cmp/cli/visualize_eeg_pipeline_outputs.py                  --bem_file /path/to/sub-01_task-faces_bem.fif                  --fs_subject sub-01                  --fs_subjects_dir /path/to/derivatives/freesurfer-7.1.1
   

5. Display BEM surfaces and source position on T1w

$ python cmp/cli/visualize_eeg_pipeline_outputs.py              --bem_file /path/to/sub-01_task-faces_bem.fif              --fs_subject sub-01              --fs_subjects_dir /path/to/derivatives/freesurfer-7.1.1              --src_file /path/to/sub-01_task-faces_src.fif

6. Plot the noise covariance

$ python cmp/cli/visualize_eeg_pipeline_outputs.py              --epo_file /path/to/sub-01_task-faces_epo.fif              --fs_subject sub-01              --fs_subjects_dir /path/to/derivatives/freesurfer-7.1.1              --noisecov_file /path/to/sub-01_task-faces_noisecov.fif

cmp.cli.visualize_eeg_pipeline_outputs.create_parser()

Create the argument parser of visualize_eeg_pipeline_outputs python script.

Returns

p – Argument parser

Return type

argparse.ArgumentParser

cmp.cli.visualize_eeg_pipeline_outputs.create_roi_labels(mean_rtc, fs_subject, fs_subjects_dir, atlas_annot, roi_tsv_file=None)

Create list of labels depending on the employed EEG pipeline (Cartool vs. MNE).

Parameters

• mean_rtc (numpy.Array) – Numpy array containing the ROI time-series

• fs_subject (str) – Freesurfer subject directory

• fs_subjects_dir (str) – Freesurfer subjects directory

• atlas_annot (str) – Basename of parcellation annotation file

• roi_tsv_file (str) – Path to parcellation index/label mapping TSV file

Returns

• mean_rtc (numpy.Array) – Numpy array containing the ROI time-series

• roi_labels (list) – List of ROI labels in the order of the rows of mean_rtc

cmp.cli.visualize_eeg_pipeline_outputs.main()

Main function that load and display different outputs of the EEG pipeline using MNE visualization features.

Returns

exit_code –

An exit code given to sys.exit() that can be:

• ’0’ in case of successful completion

• ’1’ in case of an error

Return type

{0, 1}

cmp.cli.visualize_eeg_pipeline_outputs.plot_roi_time_series(mean_rtc, roi_labels, t_min, t_max, title=None)

Display ROI time series as a carpet plot.

Parameters

• mean_rtc (numpy.array) – Numpy array containing ROI time series

• roi_labels (list) – List of ROI labels

• t_min (float) – Relative start time in sec. (x-axis)

• t_max (float) – Relative end time in sec. (x-axis)

• title (str) – Title of the figure