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).