Dear Ralf,

great that the other issue was resolved.

I just ran into the same issue �index exceeds matrix dimensions� today in a different context, and most likely it arises because not enough voxels survive in that second mask. Specifically, there are less voxel time series in the original data than PCA components (+1 for the mean) requested. I will catch this error in the next release, but for now you could just try to set a more liberal mask threshold (e.g., 0.9 or 0.95) and less erosion (if you used more than 1 voxel).

You could check that by computing sum(roi(:)>0) before the PCA computation.

All the best,
Lars