Hi Sylvain. Yes, we're doing that, and will try your suggestion about checking the first few components. I'm not sure how to test how well it works for something like connectivity analysis. We have results but are not yet sure if they are sensible. We're continuing to explore.
The problem we're running into for one of the sleep projects is that we want to use subject-space volume ROIs, which can't currently be read in on the mixed models. I the past I avoided the problem (for the auditory projects) by using surface ROIs from one of the freesurfer atlases (which works) and then adding subcortical ROIs based on growing small scouts from seed points based on MNI coordinates, using the MNI-to-subject transformation. That works for roughly spherical regions but now I have more complicated thalamic regions defined by DWI I think we're stuck using the full volume models. (Do you know of anyone who's used thalamic surface models? I don't know if that's reasonable.)
Thanks,
Emily