I am using the AAL1 brain atlas to identify my ROIs and get the number below in the connectivity matrix, as far as I understand from the connectivity tutorial this number doesn't reflect my data.
When I use the function [GetConnectMatrix] I get a 4D matrix the first two dimensions are two sets of signals A and B what do these signals represent?
3)I am using Power spectrum density (Welch) to get the source power for my ROIs and I get 94 ROIs as below but the AAl Atlas as identified in brainstorm has 99 regions
It was mentioned in a previous question: "To my knowledge, there are still no tools working correctly for connectivity analysis on unconstrained source models (3 dipoles with orthogonal directions for each 3D location). Therefore, I recommend doing your source analysis with constrained locations and constrained orientations." Help for connectivity pipeline - #3 by Francois
but I am using volume source localization so I cannot use constrained
The size is correct, MSC is symmetric connectivity metric, so only the lower triangle and the diagonal of the connectivity matrix are stored (all the other elements are redundant). Thus for 99 Scouts, 4950 elements are saved: these are the lower triangle (without diagonal) with 4851 elements ((99*99) - 99) / 2, and the 99 diagonal elements.
Those dimensions are the same as the number of Scouts, as you are computing connectivity NxN.
If you are using the same Atlas, you should have the same number of Scouts.
Please be sure that ALL the Scouts are selected in the GUI. In this example, one Scout is not selected, sometimes it is not as obvious, as unselected Scouts may be down in the list.
Are there any documents I need to read to extract source power and connectivity for my ROIs using the parameters in the image to calculate the source?
And do I need to change the default parameters for source computation?
The steps to compute the spectral power and connectivity will not change if the sources are computed with different parameters. Check the links shared above, and let us know if you have any further question.
This depends on your research question, as you know there is not a "default" way to estimate sources.
