I have ran most of my data analysis using brainstorm, but now I'll need to switch to Pyhton for some additional statistical steps not currently developed in BST.
Specifically, while computing the forward solution from my overlapping spheres in BST is it possible to get the output as a .fif file (rather than export it from brainstorm in a .mat?).
Exporting .fif files is something we still cannot do, but that we really have to develop…
We would like to have a wrapper to call easily MNE-Python functions from Brainstorm, similarly to what we’ve done for FieldTrip. We almost got someone to work on this twice, but it still didn’t happen. If nothing moves, I’ll need to work on it, but maybe not before the summer.
It would be awesome if you would like to help with this task, I guess you could count on help from both sides (MNE and Brainstorm). The idea would be to write two sets of conversion functions, one that exports Brainstorm strutures to MNE-Python objects (or worst case scenario: .fif files - but we’d like to avoid writing the intermediate files on the hard drive), and the other one that converts back the results and saves them to the Brainstorm database. Same logic as for all the out_fieldtrip_.m and in__fieldtrip.m functions.
You can very easily manipulate Python objects and call Python functions from Matlab.
You can find a simple example in the folder brainstorm3/python. I didn’t go much further than the proof of concept, but at least I am sure this Matlab-Python integration now works beautifully.
Let me know if your interested.
I have been thinking about this for weeks!
So, I have reached out to a couple of people that might be willing to help;
Personally, I am not feeling confident with my coding skills to perform such a big job (and I am also swamped with work until mid-May);
I'll keep you posted;
Keep it up!