Hello,
I need some help understanding why the function to convert optical density to haemoglobin concentration (ie mne.preprocessing.nirs.beer_lambert_law) is using the partial pathlength factor (PPF) rather than differential pathlength factor (DPF).
And more particularly, where do we get that value from?
In the tutorial “Preprocessing functional near-infrared spectroscopy (fNIRS) data” the value is given as 0.1 but elsewhere (Artinis blog) I have seen a value of 6 given. And to add to my confusion, Whiteman et al 2018 quote values of 1.8(ish) for adult males and 2.45 for adult females.
Even worse I am analysing baby data! So what number to use?
I will be happy with an understanding of the situation in adults to start with…
Many thanks in advance @rob-luke as always I would value your help
As you’ve noticed there is no concensus on what the ppf value should be, and the best choice is likely dependent on the population and anatomical region. So you will need to examine the recent literature relevant to your study.
MNE-Python exposes the ppf value (rather than hard coding it to a specific value) to allow you the flexibility to set it to the most appropriate value for your research. We use ppf to be inline with Homer and NIRS-Toolbox.
The default value for the ppf in MNE is 6, which is the same as Homer. You can see the recent discusison about this at: https://github.com/mne-tools/mne-python/pull/984. Personally, I previously used a value of 0.1 for my adult studies, but moving forward, I will use a value of 6.
Thanks Rob,
that clarifies things as does the github discussion - so essentially the partial volume correction (PVC) is being set to 1 ie ppf = [dpf=6]/[pvc=1] = 6
I would like to go back to Julia Wunderlich’s question regarding the choice of PPF vs DPF when converting optical density fo haemoglobin concentration since I am not sure it was fully answered. Given that most literature on the effects of age and wavelength has focused on DPF, it seems that PPF would be more difficult to estimate accurately. Why using PPF instead of DPF in MNE?
Thank you all for this helpful discussion!
Does anyone know the DPF or PPF value used in Hitachi ETG-4000 machine to generate the output hb files? the values are different from the output hb files converted from raw hitachi MES files using nirs toolbox. They were very different when I used the default PPF of nirs toolbox (0.1), but after putting it =6, the values are now similar but not exactly the same. how can I know if my converted hb data is correct? Is it better to use hitachi hb files?
