Hello everyone!
I have a question about preparing structure for connectivity analysis on sources.
My pipeline:
preprocess and epoch data
create headmodels, using template MRI file
perform source analysis using lcmv, but not on averaged epoch data, i want to to this on eachepoch separately
parcel the reconstucted source data onto atlas, im specifically interested in visual areas
create a matrix, which will contain structures from the atlas as rows and source data as columns.
perform connectivity analysis on parcellated data to atlas.
What i need help with is performing source analysis and then parcellation using MNE. Is it possible to do this on trial data, not on averaged data (since i do not have ERPs in my data)?
I have searched through posts in this community, but i did not found similar problem to mine.
I will be thankful for any help.
Best regards,
Monika
Yes, you can do this. I use more or less the same pipeline to analyze epileptic slowing.
By invoking the mne.minimum_norm.apply_inverse_epochs function on the epochs object you obtain the source localized epochs. (It might be helpful to set return_generator to True so as not to flood your memory).
Afterwards, you can call mne.extract_label_time_course on the sources to get the time courses in a parcellated brain and continue with your pipeline as you wish!
Okay, that is really helpful, thank you!
Looking through functions you’ve mention i’ve seen i have to use make_bem_model function, but it requires FreeSurfer subjects reconstructions - is it possible to use MRI file instead of FreeSurfer? I have one MRI file template which i want to use. If not,
For a source reconstruction, you’ll need a source space derived from MRI data. I use the FSaverage template myself that is incorporated in MNE, but you could check for other atlasses that match the one you have.