I think i've figured out what the problem was: I tried to do one-sample t-tests from the design matrix above. If now instead I only use the design matrix for doing between-group t-tests and run the one-sample t-tests separately with the -1 option for randomise this work. I was just assuming it would also work in one large contrast design matrix to get randomise to do both (like FLAME does). but happy it's working now :)
ps: I'm calling randomise like this:
randomise_parallel = -i ${newCompFile} -o ${resultsFile} -d ${desListDir}/${ides}.mat -t ${desListDir}/{ides}.con -n 5000 -T -m ${maskFile}
and this is in a loop over the different (25) ICA components and designs (30).
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