Hi Jeff,

In some of the latest releases we added to the default pipeline a "session-specific centering" step before realignment (which applies a simple translation to all functional runs before running realignment) which in our experience helped make realignment more robust avoiding or minimizing this sort of issues. Have you tried if that helps in your case as well? (alternatively, of course, you can run preprocessing separately for each session, as Herberto was doing and similarly to what one would do in the context of longitudinal data, but often that is reserved to cases where the anatomy itself may be expected to have changed between sessions, like in long developmental datasets, in pre/post surgery designs, etc.; and btw the way in batch to run preprocessing only within a single session is to set BATCH.Setup.preprocessing.sessions=session_number)

Hope this helps

Alfonso

Originally posted by Jeff Browndyke:

Hi,

Did you ever find a solution to this problem and how did you import the separately realigned and processed files back into CONN?

I've been running into this problem for quite a few people in our pipeline.

Thanks,
Jeff