On Wed, 23 Mar 2005 09:05:20 -0500, Satrajit Ghosh
<[log in to unmask]> wrote:

>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.

The problem isn't mathematical, really.  By linear algebra convention,
matrices don't have empty columns.

The issue is rather a computing language issue:  It would be convenient if
columns could be designated as empty.  I came across this problem while
scripting SPM2 stats to speed up design specification for some users with
unbalanced designs---if empty columns were allowed, I could specify the
order of conditions independently of runs (i.e., sessions).  (This could
be done by making the columns of the design matrix elements of a cell
array.)

The way SPM is written, however, the columns can't be empty (which of
course is perfectly reasonable).  Therefore, as I believe Jan Gläscher
implied, you have to batch or script around this.

>
>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) ...