Dear David,

For one-dimensional contrasts (e.g. t-tests) SPM asks you for two parameters for Bayesian inference at the second level (i) Effect Size Threshold (Default 0.1) and (ii) Log Odds Threshold (Default 10).

Other reasonable choices would be 0 and 3.

The effect size threshold, T, tells SPM that you are only interested in voxels with contrast values C^beta > T. ie. that your experimental effect is bigger than T.

The Log Odds Threshold, L, tells SPM that you are only interested in voxels where SPM is sure (with posterior probability 1/(1+exp(-L)) )

that this is the case.

Note that L=3 gives you p=0.95.

L=10 is much, much more stringent giving p=0.99995.

I would advise you use the most recent version of SPM when doing this.

Also, you don't have to do a first level Bayesian analysis if you want to a second-level one.

All the best,

Will.