Hello CONN experts,

I would like to use batch scripting for a gPPI analysis on task fMRI data.

-I have 2 groups (training, control) with a pre- post- design (2 sessions x 2 runs each)
-onsets in a .mat file from 9 trial types
('first','repeats', lures_correct, 'lures_incorrect' x 2 stimuli categories, & 'scrambled' (baseline)

I want to run seed-based gPPI to check differential connectivity, specifically for the training vs control condition for certain contrasts (e.g. lures vs repeats).

I am not sure how I can define the 1st level and 2nd level contrasts in the conn.batch:

1)  to assign the variables/onsets to be used for the 1st levels contrasts -> I do this at the setup.conditions.
(right?)

But which field do I have to specify to define the 1st level contrasts (between the trial types e.g. lures vs repeats), to create 1st level gPPIs?

2) How one can define the 2nd-level contrasts to represent the 2 different sessions X 2 runs each?
i.e.,how do I point to the different sessions, runs for my intended design?


MY CODE SO FAR:
A) to define the 9 trial types onsets via the set.conditions: 
for nsub=1:NSUBJECTS
for nses=1:2
clear onsets
load(EVENTS_FILE{nses,nsub}) %loads onsets+CondNames
batch.Setup.conditions.names=CondNames;

for ncon=1:9 %size(CondNames,2) %9 cons i.e.
for nrun=1:2
batch.Setup.conditions.onsets {ncon}{nsub}{nses+nrun} =onsets{nrun,ncon} %thus nses goes to =4; (1-2=ses1(runs1-2); 3-4=ses2);
batch.Setup.conditions.durations{ncon}{nsub}{nses+nrun} =0; % session-specific conditions
end
end; end; end
*******************************************************************

B)for group-level contrasts:
%create group indicators
group_train=participants.group(participants.complete==1); %is it ==1 training?
group_control=group_train; %copy first.
group_control(group_train==1)=0;
group_control(group_train==0)=1; %code control cond with 1s (to use in the design matrix)

BATCH.Setup.done=1; %(runs the initial data extraction steps)
%DEFINE
BATCH.Setup.subjects.names={'group_train','group_control','age'};
BATCH.Setup.subjects.effects{1}=group_train;
BATCH.Setup.subjects.effects{2}=group_control;
BATCH.Setup.subjects.effects{3}=subs_age;
%between subjects
BATCH.Results.between_subjects.effect_names={'group_train','group_control','age'} %cell array of second-level effect names
BATCH.Results.between_subjects.contrast=[1 -1 0]; % % contrast vector (same size as effect_names)
%betw. conditions (within-subjects i.e.)
BATCH.Results.between_conditions.effect_names=CondNames; %cell array of condition names (as in Setup.conditions.names)
BATCH.Results.between_conditions.contrast=[0 -0.5 0.5 0 0 -0.5 0.5 0 0] %lures correct - repeats across object&scenes (9 trial types thus 9 columns)
**************************************

Any help would be very welcome! :)