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brainets / frites

Framework for Information Theoretical analysis of Electrophysiological data and Statistics
https://brainets.github.io/frites/
BSD 3-Clause "New" or "Revised" License
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Interest in merging work into mne-connectivity? #24

Open adam2392 opened 2 years ago

adam2392 commented 2 years ago

Hi,

I spoke with the MNE core dev team earlier and we saw that you built a package on top of MNE-Python. Exciting!

We recently moved all the connectivity submodule into a new package called mne-connectivity (https://github.com/mne-tools/mne-connectivity). We've made some abstractions for data structures concerning connectivity and also have a CI/unit-testing pipeline in place with MNE. In favor of trying to pool resources together and have a 1-stop shop for MNE connectivity type analyses, would you be interested in joining forces with mne-connectivity?

Lmk if I missed anything.

PS. I did a year at Aix-Marseille actually 2017-18 under a fellowship during my PhD :p

cc: @drammock

EtienneCmb commented 2 years ago

Dear @adam2392,

Following our discussion, @ViniciusLima94 did a remarkable job during the BrainHack in implementing and documenting the single-tial coherence / PLV following MNE-Python format. See here the conn_spec function

adam2392 commented 2 years ago

That's awesome! Per our discussion in https://github.com/mne-tools/mne-connectivity/issues/57 do we still want the basic spectral measures inside mne-connectivity with a lightweight wrapper to Frites?

If so, would it be okay with you if I copy the implementation there and give @ViniciusLima94 credit of course into mne-connectivity, and then help PR here to Frites to simplify the code and just call those functions? I can add that to my list of things to do in our consolidation.

EtienneCmb commented 2 years ago

Hi @adam2392 !

That's awesome! Per our discussion in mne-tools/mne-connectivity#57 do we still want the basic spectral measures inside mne-connectivity with a lightweight wrapper to Frites?

Yes, indeed, it might be better to have them inside MNE. I think we're also going to keep the implementation inside Frites because @ViniciusLima94 might want to experiment with it (e.g. include a bias correction, maybe add the possibility to have frequency dependent kernel smoothing size etc.).

If so, would it be okay with you if I copy the implementation there and give @ViniciusLima94 credit of course into mne-connectivity, and then help PR here to Frites to simplify the code and just call those functions? I can add that to my list of things to do in our consolidation.

For me it's ok and I saw with vinicius, he's also ok. Once you'll adapt it to your format, maybe you could just tag both of us and we'll see how to best wrap it inside Frites (or if we want to keep it like that for experimenting).