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.


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]>

>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
>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