Thank you for your prompt reply, but we are still not clear on some things. Let me eloborate.
Here is our main question: Is there a difference between our fixed ISI paradigm or our jittered ISI paradigm?
This question can be broken up into: Is there a difference between our fixed hits-miss contrast and our jittered hits-miss contrast?

We originally tried to run our 3-way ANOVA -type 5 as follows: we would have factor a be our condition (fixed or jittered), we would have factor b be our task response (hit or miss), and factor c would be our subjects, nested in factor a.
With this ANOVA we found that we could not answer the second question above, what is the difference between the two contrasts of our fixed and jittered condition. A -bdiff would subtract all misses from all hits, without regrad for their respective conditional origin.
In our original post question 3 asked if we could put our hit-miss per subject contrasts as input into the ANOVA. We are not sure if labeling the hits-misses from our fixed subjects and the hits-misses of our jittered subjects as level 1 and 2 of factor b would be okay. If so could we just run -bdiff to get the difference of the contrasts of our fixed and jittered conditions?

In terms of question 1 in our original post we were wondering if afni can host a conjunction analysis, aka an analysis that identifies effects that are jointly significant in particular voxels and are not significantly different in other voxels. We were thinking that this might be a good way to create a map containing voxel wise statistics that show each voxel that is significant in both experimental designs. Any thoughts on the subject would be much appreciated.

We apologize for the length of our post, but it is needed to represent the depth of our misunderstanding.

Thank you so much for your time!
Jeremy