It seems that PTT based on the ABP & ECG signals is ~300 ms, but when based on the PPG signal then PTT is ~550 ms (consistent for multiple subjects). As I understand both ABP and PPG were measured on the arm. Do you have any idea PTT varies so much?

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I will assume you are using the MIMIC-II v3 Waveform database.

If you look at section 5.4 of the MIMIC-II user guide (warning, 2.3 MB PDF), you will see the following:

Inter-waveform alignment problems. The method used for MIMIC waveform data extraction was not designed for inter-waveform analysis. The waveform data contain unspecified/unknown filtering delays and/or unknown inter-channel delays, which may not be constant in a given record. Therefore, although the ECGs are time-aligned, there may be a (changing) delay of up to 500ms between any of the other waveforms in the data. Therefore, no pulse transit times can be accepted to be true (absolute or relative).

It's worth noting that the 500ms number is probably a conservative estimate.

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