I was also able to get the reduced connectivity (coh) matrix for the source after applying PCA on each scout.
This looks very noisy. You will need to run some group-level statistics to extract some meaningful information.
I have another question - is there a way to arrange the regions in the order I want in the connectivity matrix?
This is something you'll need to do manually with a Matlab script, by changing the order or the rows and columns in the following field of the connectivity file: RefRowNames, RowNames, TF.
- https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting
- https://neuroimage.usc.edu/brainstorm/Tutorials/TimeFrequency#On_the_hard_drive
- PTE: How is the connectivity matrix stored? - #2 by Francois
- How the Corr matix is saved?
- https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity2#Additional_documentation