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HI Leighton,
If you want to understand how randomise works in the presence of nuisance
covariates, I suggest you read the statistics papers cited on the
randomise web page, as it is rather technical, and not easy to explain.

cheers,
-MH

-- 
Michael Harms, Ph.D.

-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.		Tel: 314-747-6173
St. Louis, MO  63110			Email: [log in to unmask]




On 4/25/13 6:45 PM, "Leighton Barnden" <[log in to unmask]>
wrote:

>With your help I now have the correct data & covariate input formats for
>randomise. The next hurdle could be trickier though. I want to generate
>TFCE stats for clusters from a simple regression (with severity),
>adjusting for 2 nuisance covariates (global signal level and age). From
>the 'randomise' (theory) wiki :
>
>"Permutation tests rely on an assumption of exchangeability; with the
>models above, the null hypothesis implies complete exchangeability of the
>observations. When there are nuisance effects, however, the null
>hypothesis no longer assures the exchangeability of the data (e.g. even
>when the null hypothesis of no FA difference is true, age effects imply
>that you can't permute the data without altering the structure of the
>data)."
>
>This seems to imply that when the scan order is permuted by randomise the
>order of the nuisance covariates does not follow. If the nuisance
>covariates were always attached to the same scans would not this satisfy
>'complete exchangeability of the observations'? Could this be made an
>option (the default?) for handling of nuisance covariates by randomise?
>Incidentally, inclusion of '--tfce_H 2 --tfce_E 0.5 --tfce_C 6' on the
>randomise command line causes it to fail (FSL5.0).
>Thanks  Leighton