Physiological peak data in BIDS

1

Hi All,
I am BIDSifying a dataset that contains PPG, respiratory and ECG data. In addition to the continuous recording files, there are files containing detected peaks, i.e. scanner-side identification of heart beats and breath cycle peaks. Is there currently a recommended way of storing these in BIDS?

Thanks,
Joe

2

What’s the format for PPG?

3

I’m attaching example files here. PPGData is a continuous recording and PPGTrig is one of the peak files I was asking about. I can get more info about the acquisition if that would be helpful. (Note: I added the .txt extension so neurostars would allow me to upload)PPGData_epiRT_rs_02212020-07_49_35.txt (454.9 KB) PPGTrig_epiRT_rs_02212020-07_49_35.txt (7.5 KB)

4

Okay, so it looks like PPGData is a standard time series and PPGTrig is indices. I can see a couple of options that would probably work with existing BIDS.

Assuming:

import numpy as np
import pandas as pd
cont = np.genfromtxt(PPGData_epiRT_rs_02212020-07_49_35.txt)
peaks = np.gentfromtxt(PPGTrig_epiRT_rs_02212020-07_49_35.txt, dtype=int)

  1. Encode the indices as a indicator series:

    out = np.zeros(cont.shape, dtype=np.uint8)
out[peaks] = 1

    This could be just another column in your physio.tsv.gz, and is probably the simplest.

  2. Encode as events:

    out = pd.DataFrame({'onsets': peaks * sampling rate, 
                    'durations': np.zeros(len(peaks))})

    These could be appended to an events.tsv, but you would need to make sure that they are appropriately labeled with some kind of event type, and have n/a for any other columns that might already be there.

  3. Encode as a list in the JSON metadata for the PPGData column.

5

Thanks! Do you think it’s worth adding something to BIDS at some point specifically for these types of files? Or do you think the options you proposed are good enough long term?

6

Update to others reading this: @effigies and I discussed this with our lab and the consensus was that #1 is a good solution and there’s probably no need to make any changes to BIDS regarding this issue.

7

I like both option 1 and 2, but can imagine that something will need to come up for https://bids.neuroimaging.io/bep020 on eye tracking as well (for saccades and blinks, which are often detected in real time). Perhaps you can check there.