Hi,
On 24 Nov 2008, at 06:26, Emma Bendall wrote:
> Hi Steve and FSLers,
>
> I have run into a problem that I hope someone can shed light on. I
> refer to
> the design matrix in my previous email (below) with additional
> contrasts to
> allow for testing for negative as well as positive correlations. To
> reiterate, I am using a paired t-test on FA data obtained for a
> group at two
> separate time points with an additional EV (behvioural difference
> scores,
> demeaned and orthogonalised wrt EV1). The FA data was processed
> using TBSS.
> The design matrix is similar to:
>
> Inputs Group EV1 EV2 EV3 EV4 EV5 EV6
> SessA_s1 1 1 1 0 0 0 -2.25
> SessA_s2 1 1 0 1 0 0 -2.25
> SessA_s3 1 1 0 0 1 0 0.75
> SessA_s4 1 1 0 0 0 1 3.75
> SessB_s1 1 -1 1 0 0 0 2.25
> SessB_s2 1 -1 0 1 0 0 2.25
> SessB_s3 1 -1 0 0 1 0 -0.75
> SessB_s4 1 -1 0 0 0 1 -3.75
>
> With contrasts:
> EV1 EV2 EV3 EV4 EV5 EV6
> Con1 A-B [ 1 0 0 0 0 0 ]
> Con2 B-A [ -1 0 0 0 0 0 ]
> Con3 A-Bmod+ve [ 1 0 0 0 0 1 ]
> Con4 B-Amod+ve [ -1 0 0 0 0 1 ]
> Con5 A-Bmod-ve [ 1 0 0 0 0 -1 ]
> Con6 B-Amod-ve [ -1 0 0 0 0 -1 ]
>
> Firstly, is it correct to simply include Con5 and Con6 to obtain
> negative
> correlations, or should I alter the design matrix in some way?
The design matrix is fine but contrasts 3-6 aren't right. A sensible
contrast would be
[0 0 0 0 0 1]
which tests for positive correlation with the behavioural difference.
It doesn't really make sense to include EV1 and EV6 in the same
contrast - the results will be hard to interpret, as you found.
Cheers.
>
>
> Secondly, assuming the above matrix and contrasts are correct, is it
> possible that a small n (e.g. n = 5) could be responsible for FSL
> randomise
> outputting contradictory results that survive cluster thresholding and
> additional Bonferroni correction? For example, I ran randomise using
> the
> above design and contrasts with cluster threshold of 3 and 10000
> permutations. A cluster resulting from the Con4 test overlapped
> (almost
> completely, though it was about 40% the size of) a cluster resulting
> from
> the Con3 test. I checked all_FA_skeletonised voxel values within each
> respective cluster (using fslmeants with -showall option and
> standard stats
> software) and conclude that the Con4 result is incorrect. The other
> results
> seem reasonable, however I should probably abandon the test procedure
> altogether given that randomise has output what seems to me to be at
> least
> one nonsense result.
>
> A similar situation occurred recently with a test group of slightly
> larger
> n, where a cluster from Con6 (negative correlation) overlapped with a
> cluster from Con4 (positive correlation). Again I suspect the small
> n is the
> source of my problem, but I'd be grateful for any further insight or
> suggestions regarding how randomise might be coming up with these
> contradictory results.
>
> Thanks,
>
> Emma
>
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR 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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