Alfonso.

Thanks you for reply. I have some more follow-up questions.


I successfully ran a batch script for the entire process, setup, preprocess, analysis, results. In my the script, I called conn_batch twice. I assigned everything to a BATCH (all caps) variable from setup through analysis. Then, I ran the command conn_batch(BATCH). I set up another batch (lower case) variable  and then ran the 2nd level analysis with the steps you outlined in your first replay as such for the 3 contrasts with parenthesis and not the curly brackets. In the second batch variable, in included batch(ncondition).Results.filename line specifying the Batch.filename created in the setup. So, that was my work around before I read you latest reply. The output provided the 3 different contrasts, CondA vs CondB, CondA vs CondC, CondB vs CondC.

I tried running the entire script with the curly  brackets you suggested in your most recent reply. I received an error message.

Cell contents assignment to a non-cell array object.

Error in batch_conn (line 255)
BATCH{1}.Results.between_subjects.effect_names={'AllSubjects'};


but then I realized you had a clear BATCH line before setting the BATCH{} variables. Is this the step needed to run multiple contrasts? It appears similar to my workaround where I just created a 2nd variable to assign values for my 3 contrasts and calling conn_batch a second time in my script.If so, I would also need to provide the *.mat filename (BATCH{1}.Results.filename ='name_file.mat') containing all of the preproc/setup/analysis/ information, no? 

...

A separate question about the batch process is when I don't specify a contrast at all. The manual states it will run a 2nd-level analysis for each condition. However, my output only gives one 2nd-level result for one condition. It runs the analysis 3 times, but overwrites the results file. Should I just exclude the overwrite command below? Would that provide a results output folder for each condition if I excluded that line?

BATCH.Results.between_subjects.effect_names={'AllSubjects'};
BATCH.Results.between_subjects.contrast=[1];
BATCH.Results.done=1;
BATCH.Results.overwrite='Yes';  %Excluded This line????
BATCH.Results.foldername =conn_results_folder;

Thanks again for all of your help.