I would caution against putting multiple basis functions in your second-level GLM. As you soon as you add multiple observations per subject, the analysis becomes a repeated-measures analysis AND the only valid comparison is comparing the levels of the factor against each other (e.g. basis function 1-basis function 2); comparing them against 0 isn't valid (e.g. basis function 1>0). The reason for this is that the error term represents the within-subject error.

I am not sure why you'd want to test if the basis functions are different (e.g. canonical HRF amplitude is different from the temporal derivative).

On Tue, Jan 14, 2014 at 2:26 PM, gj <[log in to unmask]> wrote:

Hi,

I apologize for the following very naive and big-no-no/way-too-general question...but time crunch is getting painful... I'd like to
understand how covariance/hyperparameter/nonsphericity calculations are PRACTICALLY handled in SPM (i.e. structures, code) so I can properly set up SPM.xVi.Vi and SPM.xVi.I in a Matlab script for a 2nd level analysis with 3 basis functions (and hence I should have 6 hyperparameters if I only have a single contrast in my 2nd level design, but I'm failing to set this up properly....and as far as I understand, I need to make sure that xVi.Vi is an nxn matrix, such that n=#observations, so if I take a single contrast from 1st level with 3 basis functions and 10 subjects, this would be a 30x30 matrix?)....

Any pointers/guidelines/thoughts and your patience greatly appreciated!!