Hi everyone,

Firstly, sorry if this topic has previously been treated.

I am trying to understand why I get different results after SPM and CONN 2nd level analysis.

I am doing something quite easy: 
In CONN I have: [1 -1] in between-subjects contrast (I have two groups), [1] between-conditions contrast (is a resting state fMRI) and [1] between-measures contrast (Intrinsic Connectivity).
In SPM I performed a two-sample t-test 2nd level with CONN first level outputs. 

No other covariables were added in any of the cases. Results are not completely different but peaks are not the same, clusters sizes are different, even the number of survival clusters (at the same threshold) differ depending the software.

Does anybody have any idea of where could the problem be? 

Thank you in advance,

Ines