Hi Alfonso and everyone,


I am having a problem with the Realignment and Unwarping preprocessing step when fieldmaps are available.

To keep it short, in some subjects, this step fails and produces bad realignments... In fact for some subjects, it's quite bad, with the upper part of the brain being completely cut (see attached file, top realigned, bottom original). Once I re-run the preprocessing, without actually changing anything (from the same starting files), it can produce different results, and in fact work properly...

I don't know if this is a known problem with this particular step. Should we always check and repeat the step if it fails?

Cheers,
Herberto

More details:
I have 20 subjects, over five sessions. They do two very different tasks, and pre and post resting-state (the three processed separately, same structural always, but fieldmaps for each day).
Interestingly, the "fail" in the realignment doesn't always happen for the same subjects. For example task 1, initially it produced bad results for subjects, 2, 3, 8, and 10. Whereas for task 2, for 5 and 15.... Moreover, I already confirmed that repeating this, from the beginning for subjects 5 and 15, worked normally (as in Realign&unwarp produced good results).