Thank you very much for providing this forum for folks to ask their MNE questions! I am a PhD student using MNE and EEGLAB (and proprietary LabChart software) to process and score sleep data for seals (EEG, EOG, EMG, and ECG). I am trying to switch all of my analyses to Python to ensure reproducibility with open-source software.
Heart beat detection and heart rate calculation
I would like to detect heart beats and create an additional instantaneous heart rate channel to visualize the success of peak detection. In the past, I have used LabChart (proprietary electrophysiological analysis software) to generate “cyclic measurements” of heart rate in a separate channel. I have found
HeartPy in python but would need to get the ECG channel out of and back into MNE to use this.
I have tried
mne.preprocessing.find_ecg_events() to locate ECG events. However, I need to customize the
qrs_threshold given that the seals’ heart rate can go down to 2bpm and up to ~120bpm. What do the numbers 0-1 mean for this variable?
I have not yet found an easy way to add a heart rate channel in MNE to visualize the success of
find_ecg_events() at peak detection. Would you recommend using MNE for heart rate processing or switching to another software or package and then appending a separate channel to the EDF?
Here are the settings I have been using in LabChart:
I’m wondering if there is a way to apply ICA to remove heartbeats from EOG, EEG, and EMG, but maintain the ECG channel intact, and construct two additional channels: one “reconstructed ECG” (append the ECG component(s) which was subtracted from the other channels - similar to ica.find_ecg_events) and one “reconstructed brain” (append the component(s) which seemed to have most of the brain signal). I have used EEGLAB in the past and it has a function to append those components, but I do not know the relevant names in MNE. I would like to append ICA001 or similar from
I need to create a custom topography map for the location of sensors on the animal, should I only generate this map for sensors on the head or should I include EMG and ECG sensor locations further down on the body? How would you recommend constructing this map from scratch (with distances in centimeters between each electrode)? The ultimate goal would be to use this topomap to demonstrate that ICA successfully isolates artifacts from the ECG channel.
Thank you very much for any help or guidance that you can provide.
- MNE-Python version: 0.23.00 (just updated- thanks!)
- operating system: Windows 10