Rik and James,

It is funny that this should come up, a PhD student in our lab had a similar
problem with columns of her design matrix with parametric modulation that
some of the columns disappeared for some of the subjects. It turned out,
after looking more carefully, that the randomization she had used for the
experiment caused some of the sessions to contain only 2 or 3 of the 5
possible values of the parametric modulation. We were originally trying to
model the modulation up to a factor of three (cubic), but after we found
this we left the modulation as linear and the problem with the missing
columns was solved without having to change any of the default parameters of
SPM5 regarding orthogonalisation. And I didn't have to look at where this
was occurring in the code and I was more sure that the PhD student was using
the right model. 

Hope this sheds some insight.
Best,
Virginia


On Tue, 6 Jan 2009 14:14:49 +0000, Rik Henson <[log in to unmask]>
wrote:

>James -
>
>Firstly, just to clarify for others - SPM does not perform any
>"auto-orthogonalisation" of regressors, except when using multiple
>parametric modulations of the same condition.
>
>If you have multiple parametric modulations of the same condition and
>these are (partially) correlated, this is not necessarily a problem.
>Only if they are linearly-dependent is there a problem, which should
>lead to blank regressors *with* orthogonalisation (not after turning it
>off?), so I am a bit puzzled by your email (I am also confused why you
>have different numbers of columns - I wasn't aware that SPM would ever
>do this?). So is there something else going wrong with your batch
>creation of design matrices?
>
>More generally, you do not necessarily need to be concerned about grey
>bars indicating that betas for some columns are not estimiable unless
>you are interested in contrasts like [0 1 0 0 ...] on just that column
>(eg other contrasts, like [0 1 0 -1...] might well be estimiable). But I
>assume you are interested in the former type of contrast (eg on a single
>parametric modulator) and one way that you can bypass the contrast
>manager's check is to define and estimate the contrast by a direct call
>as below:
>
>    SPM.xCon(n) = spm_FcUtil('Set',cname,'T','c',c,SPM.xX.xKXs);
>    spm_contrasts(SPM);
>
>where n is the next contrast number and c is the contrast (column
>vector) you want to estimate (and 'T' can be 'F' instead). The
>spm_FcUtil will actually reproject the contrast to make it estimiable,
>but take care that the new project contrast is still interpretable.
>
>Rik
>
>> Dear all,
>>
>> We're currently having problems with our design matrices/contrast
>> analysis that I'd appreciate some help on. (FYI: SPM5, Matlab 7.6).
>>
>> Originally, our design matrices were occasionally showing differing
>> numbers of columns as well as grey bars indicating that the betas were
>> not uniquely specificied. Following Rik Henson's link yesterday I turned
>> SPM's "auto-orthogonaliser" off and this resulted in matrices with the
>> correct number of columns - but now showing the black lines that were
>> previously (presumably) being excluded which explained the different
>> sized matrices - many thanks for that.
>>
>> However, we still have the problem of columns that are
>> non-uniquely-specified - which cannot be used in any contrasts (the
>> contrast manager will not permit a "1" on any columns that had this
>> (grey box)).
>>
>> Rather than explain the whole design, I wondered if anyone had any good
>> advice on how generally to deal with betas not being uniquely specified
>> - for example, is it best to drop the whole session? Can the contrast
>> manager's refusal to run be over-ridden?
>>
>> I want to be able to batch process the contrasts and so ideally don't
>> want to end up with different columns numbers with different parameters
>> for each subject etc as this would mean I'd have to manually enter
>> contrasts for each subject and with N=36 that'd take some time.
>>
>> If anyone has any thoughts on the best way forward that would be much
>> appreciated.
>>
>>
>> James Gilleen
>> IOP
>> London, SE5 8AF
>> tel: 0207 848 0542
>>
>
>--
>
>-------------------------------------------------------
>                 Dr Richard Henson
>         MRC Cognition & Brain Sciences Unit
>                 15 Chaucer Road
>                   Cambridge
>                  CB2 7EF, UK
>
>           Office: +44 (0)1223 355 294 x522
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>
>http://www.mrc-cbu.cam.ac.uk/people/rik.henson/personal
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