Hi Darren, I think there are two separate issues here.
1. The design is rank deficient I suspect because you are attempting to
model every timepoint with some condition. Because the data is demeaned
you are not allowed to do this - unless you have a natural single "rest"
condition then you need to define one of the conditions as rest and work
with respect to this. OR it maybe that your design is ok, just _nearly_
rank deficient - what deficiency ratio is it giving you?
2. With your "C vs L&M" - you are asking
Cr - mean(Cq+Ca+Lr+Lq+La+Mr+Mq+Ma)
would
[ Cr - (Cq+Ca)/2 ] - { [ Lr - (Lq+La)/2 ] - [ Mr - (Mq+Ma)/2 ] } / 2
be more sensible or am I missing the intension of the question you are
wanting to ask with this question?
Thanks, Steve.
On Thu, 22 May 2003, Darren Schreiber wrote:
> I am trying to replicate some event-related analysis in FSL that I did
> with UCLA's AIR tools and I am getting an error that my design is rank
> deficient.
>
> Here is the setup:
>
> I have seven types of questions A,C,L,M,R,T,U. The TR is 4 and I
> collected three volumes for each question (the question, the answer,
> and the rest: q, a, r).
>
> In the AIR tools, I specified three contrasts of C vs L & M, L vs. C &
> M, and M vs C & L. I included all three volumes (qar) in the contrast
> design as follows:
>
> C vs L&M:
> q a r
> C -1 -1 8
> L -1 -1 -1
> M -1 -1 -1
>
> L vs C&M
> q a r
> C -1 -1 -1
> L -1 -1 8
> M -1 -1 -1
>
> M vs C&L
> q a r
> C -1 -1 -1
> L -1 -1 -1
> M -1 -1 8
>
> The results fit substantive expectations beautifully. But, I want to
> take advantage of FSL's mixed effects abilities.
>
> So, I specified nine EVs corresponding to Cq, Ca, Cr, Lq, La, Lr, Mq,
> Ma, Mr. And, I tried to set up the contrasts like I had in the AIR
> tools.
>
> C vs LM -1 -1 8 -1 -1 -1 -1 -1 -1
> L vs CM -1 -1 -1 -1 -1 8 -1 -1 -1
> M vs CL -1 -1 -1 -1 -1 -1 -1 -1 8
>
> What am I doing wrong? How do I replicate the AIR results in FSL?
>
> I have verified that the custom 3 column files specifying the timing of
> the EVs is correct.
>
> Of course, I know that EV1, EV2, and EV3 are not independent, but I am
> not sure how to replicate the AIR results without setting up the same
> contrast.
>
> By the time I get to the course in Marina del Rey, I will have a very
> good understanding of FSL, I think. But, since I have to have my data
> analysis done for a deadline before the class, I appreciate your
> indulgence with the ceaseless barrage of questions.
>
> Darren
>
Stephen M. Smith MA DPhil CEng MIEE
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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