Converting simulation output to MEG BIDS format

[george1820]

Hello,

I am currently using HNN for my masters research project and we are looking at conducting analysis in MNE using the output of the simulations. Is there currently a way for the simulation data to be converted into MEG BIDS format - as this is what the majority of my previous experience in analysing electrophysiological data is in. If not, would it be possible to create?

Thanks
George

[asoplata]

Hello George, sorry for the late response, I missed this due to a lot of grant-related deadlines we've been dealing with.

I think we need more information before we can help you, however. The "main" output of HNN is the "dipole moment" (in units of "scaled" nano-Amperes), such as in this example here. HNN can also record simulated cell spikes, LFP, CSD, etc., but you are probably most interested in the dipole moment. The HNN API (not the GUI) can export simulated dipole data to a txt file format whose specification is described in the docstring here https://github.com/jonescompneurolab/hnn-core/blob/master/hnn_core/dipole.py#L715-L732 . HNN dipole output is often compared against similar experimental output that is pre-processed by MNE, rather than being re-imported into an MEG-containing format like BIDS. Currently, HNN is not capable of exporting to BIDS filetypes or structure-types. I would strongly recommend you read this tutorial here which uses experimental data and processes it in MNE, then runs a simulation for comparison to the data using HNN. If I can help in another way, please let me know.