> OK now I'm confused, according to the manual the q value is replaced with
> z(q). Is that only done by 3dFDR and not 3drefit? I had thought that I would
> pick a level of significance, say alpha=0.05, and threshold at the appropriate
> z(q). Is that incorrect?

I assume the manual you read is about 3dFDR, which is the old approach to obtaining FDR. With 3dFDR you do get a z-value, which you can use for thresholding. However, such a z-value is provided simply for the convenience of thresholding. In other words, each z-value eventually is associated with a q-value. With the new approach of 3drefit -addFDR, the q-value is provided without the intermediate z-value.

> What I'm unclear on is how to come up with the critical q value for thresholding.

It is pretty arbitrary: 0.05 or below is generally acceptable.

> Also, when you say that the use of alphasim is moot because it assumes the
> normality of the data. Is that because the random numbers are chosen from
> a normal distribution or because of the Gaussian filtering? I should point out
> that one of the stages of the VBM is smoothing with a Gaussian of specified
> sigma, a number which I have been passing in to AlphaSim ( in the form of
> FWHM, I've only just realised that AlphaSim can take a sigma arg). Would
> that make a difference?

My suggestion of FDR was based on the fact that you used non-parametric approach for group analysis, which does not require normality assumption about the beta values across subjects. Is the reason you run non-parametric analysis in the first place because of not enough number of subjects?

Gang