Gang Chen wrote:

> If you run 3drefit -addFDR on your non-parametric analysis
> results, you should see a q value right below the p value
> underneath the slider bar on AFNI viewer. That q value is the
> corresponding FDR corresponding to each p value, and you can
> use the q value as your correction threshold in the FDR sense.

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?

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

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?