I am trying to implement this exact experimental design with the batch interface for resting state connectivity acquired from two groups before and after a treatement.  Everything seems to be correct except when I look at the onset and duration settings via the GUI. All of the onset and durations are set to 0 and 'inf' respectively. 
My batch code is at the end of this email.  The code is doing what i want it to do. When I check onset settings I have

>> batch = infConnAnalyzeInput_v2('../input');
>> batch.Setup.conditions.onset{1}{1}

ans =
[0] []
>> batch.Setup.conditions.onset{2}{1}
ans =
[] [0]

After running conn_batch(batch) the onset and durations settings for all sessions and conditions are set to 0 and inf.

What am I doing wrong?  I am also having trouble understanding the need for this setup.  Why not just define a pre and post condition?  What is the benefit of having two conditions and two treatments? 

As always thank you for your help,

Bob





for iiSession=1:2

     batch.Setup.functionals{1}{iiSession} = fullfile(preprocDir, sprintf('%d_%s',iiSession,'bold2Mni_bold.nii'));

for iiCondition=1:2

   if iiCondition==iiSession
        batch.Setup.conditions.onset{iiCondition}{1}{iiSession}      = 0; % Condition{nCondition}{nSubject}{nSessions}
        batch.Setup.conditions.durations{iiCondition}{1}{iiSession} = inf;
    else
         batch.Setup.conditions.onset{iiCondition}{1}{iiSession}      = [];
         batch.Setup.conditions.durations{iiCondition}{1}{iiSession} = [];
    end

end
end