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Dear Jan and list, Thanks you for your replies. I do have batch scripts which do pretty much what you suggest, but this is precisely what I wanted to avoid. Perhaps my matrix algebra is conflicting with my SPM estimation. To give a clearer example, lets look at the following code. a = kron(eye(2),rand(20,10)); a(:,[3,4,5,14,15,16]) = 0; [u,s,v] = svd(a); The empty columns would correspond to singular values of 0. And SPM does do a design matrix reduction to remove linear dependencies that exist. So, I don't see why specifying empty onsets is a problem mathematically. As Bas suggests and if X did have zeros in columns this estimation would be problematic. B= (X'X)^-1 x X'Y But, in SPM X is not really the created design matrix. It is a reduced form and contrasts get mapped to this reduced form. Hence, I'm trying to understand why the designers of SPM didn't allow empty conditions. Thanks again, Satra On Wed, 23 Mar 2005 12:47:32 +0100, Jan Gläscher <[log in to unmask]> wrote: > Dear Satra and list, > > SPM won't let you estimate a design matrix with empty regressors as all > the other answers have correctly suggested. I will outline a solution > for a conditional design and contrast specification below, but I must > stress that it is complicated and therefore I would therefore strongly > recommend using the batching facilities in SPM2. If you are not > familiar with batching you will find a lot of sample batch files on this > list, e.g. Karl Friston's sample file > > http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind02&L=spm&P=R282882&I=-1 > > Now, there are 3 constraints to this problem that have to be taken into > account: > > (1) There must not be any empty regressors. > (2) For a valid parametric modulation there must be at least 2 trials > (= 2 onset) in the "onset" regressors (i.e. the one where you > specify your onsets) > (3) Contrast specification is tricky (Therefore I recommend a spcific > naming scheme for your regressors (and parametric modulations) which > you can later reference) > > Here is some example code for solving problem (1) and (2) ...