Hi @ichkifa,
Thank you! Can I ask you to clarify whether you were able to replicate the preprocessing from ABIDE I, but haven’t been able replicate it for ABIDE II, or if you’re comparing ABIDE II outputs to ABIDE I outputs?
Looking at the ABIDE II documentation, it appears that there are a handful of subjects that have data in common with ABIDE I, but not all of them. Since the timeseries are therefore coming from different participants, and may also have been produced using a range of C-PAC versions and pipeline configs, they won’t be the same when comparing ABIDE I/II.