We are interested in performing a conjunction analysis in which we look for the common regions of activation for a specific condition across 2 groups of subjects.

Our experimental design consists of 2 groups, one in which event related, visual stimuli were presented at a slow, fixed interval and a second group in which the visual stimuli were presented at jittered shorter durations. We looked at encoding hits and encoding misses for each group.

1. How do we set up a conjunction analysis where we ask whether a particular voxel is signficant across both contrasts (ie, hits-misses for the jittered group and hits-misses for the fixed ISI group)?

2. If we were to set up a more traditional ANOVA, would we use 3dANOVA where the input -a is jittered duration v. fixed duration and subjects are assumed to be part of a fixed-effects model OR would be use 3dANOVA3 type 5 where the input -a is as above, and -b is hits-baseline or misses-baseline, and -c is subject. We would then ask for the -bdiff of factor -b.

3. With regard to question #2, we have assumed that it is more desirable to carry our analysis as far as possible in individual subjects, and therefore use the glt combination of hits-misses for each subject as the input into our ANOVA, rather than hits-baseline and misses-baseline. We don't think that approach would work with 3dANOVA3.
Thanks for your time!