Current Source Density (CSD) with mne-python?

[giuliagennari]

I would like to transform my EEG data from voltage into current density.
Something like this http://psychophysiology.cpmc.columbia.edu/Software/CSDtoolbox/tutorial.html
but through Python, can anyone give me some instructions?

I am a young PhD student, this would be extremely helpful!!!

Thanks a lot in advance!

[larsoner]

We currently do not have CSD estimation in MNE, but it is something we plan to implement.

@dengemann do you have time to give it a try?

[jona-sassenhagen]

Denis is married now, he's done writing code :D

[dengemann]

Epic provocations to get me coding here! You guys are married too :) My MNE coding priority is in auroreject these days and some maintenance issues. But happy to supervise / help with things.

…

On Wed, 30 Aug 2017 at 11:08, jona-sassenhagen ***@***.***> wrote: Denis is married now, he's done writing code :D — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4480 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB0fisLx2zfc_xEUNhDdfOoc-yAfscxlks5sdSaagaJpZM4Oz-yE> .

[mmagnuski]

I will need CSD in a month or so - I could try this in a few weeks, but I would need help.

[mmagnuski]

(BTW I am not married so I can still code ;) )

[agramfort]

imagine the day you have kids :)

[palday]

I took a look/thought about this a bit ....

There are some subtle data structure issues with CSD data -- they're lot like normal EEG data, except when they're not (different units, reference-free, lack of volume conduction, etc.). This leads to the obvious question of what channel type to assign them. If we let users be responsible for not doing invalid transformations on CSD data, then eeg seems like generally the obvious choice with the exception of the units, which becomes relevant for plotting. It would also be nice to somehow indicate that it's CSD data when saving and loading (it's not harmless to re-apply the CSD transformation unlike re-referencing, which is normally obvious anyway), but the FIFF format doesn't have a CSD channel type. the closest thing seems to be the ch_unit tag, but that's an enum, which doens't include uV/cm^2 as a possibility. Another option may be to include the CSD as a projection, but again, the corresponding enum doesn't have a value for it. Yet another alternative would be to treat CSD like we currently treat ICA, but the big difference there seems to be ICA.apply() yields "normal" EEG data back.

Otherwise, I think a lot of the more numerical steps for CSD could be achieved by re-factoring some existing code, e.g. parts of channel interpolation uses some of the same techniques as used in the usual CSD calculations.

[jona-sassenhagen]

I think given that we don't take care of any of these things for, e.g., the Evoked objects containing log p values, or ICA-transformed objects, I think it'd be consistent to just implement CSD for now, leave it to the user to not fuck up things here, and think about stronger support later.

@miykael

[larsoner]

As far as dealing with the FIF format goes, we can probably get away with storing the CSD transformation in raw.info['comps']. Usually this applies only to MEG, but IIUC we can store any linear transformation in there, and it will be handled properly in forward calculations, etc.

[jona-sassenhagen]

I like that option.

[transpersonify]

Is there any update on this issue?
I am looking for a python version of CSD to apply on my EEG data (I have channel x time data matrix and 2D location matrix, independent of mne layout). I found implementation suitable for LFP but not for EEG. The idea is to apply spatial smoothing at each trials as a pre-processing step. Can anyone help?

[larsoner]

It still has not been implemented AFAIK

[palday]

Nope. And as fascinating as I find it, it's not a high priority for me, neither in terms of my active research nor my programming hobby.

[sherdim]

Look at adaptaton of CSDtoolbox functions

It will be nice to get them somewhere in mne.decoding.transformer

[mmagnuski]

Good you're sharing this, I had my own adaptation of CSD tested against CSD toolbox for a some time now (https://github.com/mmagnuski/borsar/blob/master/borsar/csd.py) but I didn't have time to make a proper PR. Do you think you could do it? Because this is an adaptation we would also need to ask the original authors about licensing. I can help with testing etc. (I have some tests for this already).