Hi,

There are several ways to do the same but one simple way would be:

1) in the Setup.Basic tab simply enter 4 as the number of runs/sessions

2) then in Setup.Conditions define your four conditions (e.g. pre_treatmentA, pre_treatmentB, post_treatmentA, and post_treatmentA) and associate each with the corresponding functional scan (this association may be common across all subjects or it may be different for different subjects, for example if the order of the two treatments was randomized across subjects). 

3) last, when you get to second-level analyses, select  AllSubjects in the 'subject effects' list, then select your four conditions in the 'Conditions' list and enter a vector [-1 1 1 -1] in the 'Between-conditions contrast' field. That will evaluate the interaction between your two factors (i.e. (post_treatmentA - pre_treatmentA) - (post_treatmentB - pre_treatmentB) )

While not necessary for this analysis, you may also want to define a subject-level variable (in Setup.Covariates (2nd-level)) that explicitly identifies the order of the two treatments across subjects (e.g. define a 'TreatmentOrder' covariate and enter a +1 for subjects who received treatment A before treatment B, and -1 for the opposite-order subjects). This information is redundant with what you have already done in step (2) above, but it allows you to, for example, use this variable in your second-level analyses to evaluate potential treatment-order effects in your results.

Hope this helps

Alfonso

Originally posted by jrobinson:

Hi there,

I have a within-subjects crossover design. Each participants underwent 2 sessions, with 4 scans total (pre-administration and post-administration for 2 conditions).  I'm struggling to figure out if/how conn can handle testing for differences in post-pre connectivity between conditions.  

Any help would be greatly appreciated!