PCA explained variance from scout time series


I am extracting the scout time series (Brainnetome atlas) from source signal with PCA method. I was wondering if there was a way to get for each scout the value of the variance explained by the first PC in the ROI as a whole and also for each vertex.

Is there a way to obtain this in a matrix? Thank you for your time!


Hello @angelantonio

For the moment, this value is not saved. However when extracting the scout time series it is printed in the Matlab Command Window as:

  • For constrained sources, the explained variance value is printed for each scout. E.g.:
    BST> First component explains 40.3438% of the signal of cluster Cont_Cing_1 L.

  • For unconstrained sources, only the explained variance value for last dimension (Z) for each scout is printed. E.g.:
    BST> First component explains 83.5981% of the signal of cluster Cont_Cing_1 L.

  • In case of using PCA to flat a Unconstrained source map, the explained variance value only for the last vertex in the source map is shown. E.g.:
    First component explains 68.8834% of the signal.

We are currently in the process to update how PCA is computed in Brainstorm. Including the storage of the explained variance values may be a good option for that PCA revamping. Any thought @Marc.Lalancette?


Hello, indeed as Raymundo said, what's displayed is a bit bugged right now, but it should improve when we update the PCA. I don't think we'll store the values as it's not really compatible with our Brainstorm structures, but it should be fairly easy to recompute if needed.

If Scout is your scout PCA time series, and Sources is the original array of time series for each vertex in that scout, then the total variance "explained" is:
sum(Scout.^2,2) / sum(sum(Sources.^2,2));
while for each vertex, it would be this:
(Sources * Scout').^2 ./ sum(Sources.^2,2) / sum(Scout.^2,2);

You can get the data by right clicking in the Brainstorm tree, "file", "export to matlab". Then the actual data is in the "F" field. But it's a little bit more complicated because you need the indices of the vertices for the scout, which give you the rows of the F matrix. Sorry if it's not clear enough, feel free to ask for more details. :slight_smile: