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?
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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