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Basic usage

🧐 Prepare your dataset

MNE-BIDS-Pipeline only works with BIDS-formatted raw data. To find out more about BIDS and how to convert your data to the BIDS format, please see the documentation of MNE-BIDS.

We recommend that

  • faulty channels are marked as "bad".

    Why?

    While we do run automated bad channel detection in the pipeline, it is considered good practice to flag obviously problematic channels as such in the BIDS dataset.

    How?

    MNE-BIDS provides a convenient way to visually inspect raw data and interactively mark problematic channels as bad by using the command

    Run in your terminal
    mne-bids inspect
    Please see the MNE-BIDS documentation for more information.

  • the data is anonymized before running the pipeline if you require anonymization, as the pipeline itself does not allow for anonymization.

    Why?

    This was a conscious design decision, not a technical limitation per se. If you think this decision should be reconsidered, please get in touch with the developers.

    How?

    If you already have BIDS formatted data you can use mne_bids.anonymize_dataset. Otherwise you can use the mne_bids.write_raw_bids function of MNE-BIDS that accepts an anonymize parameter and can be used to anonymize your data by removing subject-identifying information and shifting the measurement date by a given number of days. For example, you could use

    Python
    from mne_bids import write_raw_bids

write_raw_bids(..., anonymize=dict(daysback=1000))
    to shift the recording date 1000 days into the past. By default, information like participant handedness etc. will be removed as well.

    You can also deface your MRIs with mne_bids.write_anat:

    Python
    from mne_bids import write_anat

write_anat(..., landmarks=landmarks, deface=True)
    Please see the tutorials of mne_bids for more information.

📂 Create a configuration file

All parameters of the pipeline are controlled via a configuration file. You can create a template configuration file by running the following command:

Create a template configuration file
Run in your terminal
mne_bids_pipeline --create-config=/path/to/your/custom_config.py

You can then edit the file and adjust all parameters that are relevant to your data processing and analysis.

🏃🏿‍♀️ Run the pipeline

Run the full pipeline

To run the full pipeline, execute the following command in your terminal:

Run in your terminal
mne_bids_pipeline --config=/path/to/your/custom_config.py

Run only parts of the pipeline

Run only the preprocessing steps:

Run in your terminal
mne_bids_pipeline --config=/path/to/your/custom_config.py --steps=preprocessing

Run only the sensor-level processing steps:

Run in your terminal
mne_bids_pipeline --config=/path/to/your/custom_config.py --steps=sensor

Run only the source-level (inverse solution) processing steps:

Run in your terminal
mne_bids_pipeline --config=/path/to/your/custom_config.py --steps=source

(Re-)run ICA:

Run in your terminal
mne_bids_pipeline --config=/path/to/your/custom_config.py --steps=preprocessing/ica

You can also run multiple steps with one command by separating different steps by a comma. For example, to run preprocessing and sensor-level processing steps using a single command, do:

Run in your terminal
mne_bids_pipeline --config=/path/to/your/custom_config.py --steps=preprocessing,sensor

You can directly visit our examples page to see some configuration files and the corresponding results.