Dear Ines,

Unfortunately, I did not find any other way to regress out the effect of heterogenous scanners settings. For the moment, I dropped this kind of analysis in CONN as I got unreliable and meaningless results doing so, and I am rather doing separate analyses (one per center) that I then combine using a meta-review kind of analysis such as with the PVM software (see Costafreda, S. G. (2009). Pooling fMRI data: meta-analysis, mega-analysis and multi-center studies. Frontiers in neuroinformatics, 3, 33).

I am also looking into other approaches such as ICA regression and machine learning but they are all experimental, the most reliable way currently from what I have read so far seems to be the meta-analysis approach, as it assumes independence between the analyses, it is statistically perfectly fine to compare multicentric analyses this way (just like one can compare multiple studies results).