Dear Anod,
In CONN you have the possibility to do 3rd-level analysis in the 2nd-level tab, by doing t-tests both at the sessions level and at the group level. So in your case I would input only 2 sessions per subject and setup the sessions accordingly in the "Conditions" sub-tab of the Setup tab, and create two groups (as 2nd-level covariates in the Setup tab), so that you will be able to do a 3rd-level analysis in the end as I wrote above.
I hope this helps,
Best regards,
Stephen
In CONN you have the possibility to do 3rd-level analysis in the 2nd-level tab, by doing t-tests both at the sessions level and at the group level. So in your case I would input only 2 sessions per subject and setup the sessions accordingly in the "Conditions" sub-tab of the Setup tab, and create two groups (as 2nd-level covariates in the Setup tab), so that you will be able to do a 3rd-level analysis in the end as I wrote above.
I hope this helps,
Best regards,
Stephen