Proper way to add and handle reference channels in MNE-BIDS-Pipeline

💬 Support & Discussions
1

I’m working with raw Brain Vision EEG data that was originally referenced to Cz, so this channel is not included in the data. I want to add Cz back as a flat channel and then rereference to TP9/TP10. Currently, I’m using the following approach:

  1. Use mne.add_reference_channels to add Cz as a flat channel
  2. Run the MNE-BIDS-Pipeline (eeg_reference = [“TP9”, “TP10”] → see Implementing subject-specific EEG reference in mne-bids-pipeline)

However, I’ve noticed that when I add the Cz channel before running the pipeline, the PSD plots for Raw (original) and Raw (filtered) show Cz at -3000 dB. It seems that the pipeline is filtering and plotting the data before rereferencing.

Is there a proper way to add a reference channel (Cz in this case) within the MNE-BIDS-Pipeline?

Thank you!

2

I figured out that if there is currently no such feature in the mne_bids_pipeline I can just add Cz and reference before converting my data to bids and then set eeg_reference = [ ] in the pipeline config file to skip rereferencing since it was already done.