help > RE: Realignment & Unwarping fails for some subjects
May 17, 2021  05:05 PM | Herberto Dhanis
RE: Realignment & Unwarping fails for some subjects
Hello again,

I don't know if this will help or not, but normal realignment (without Fieldmaps) works well for every subject. It's only the Realign and Unwarp that doesn't work (I have done really many many tests....). Again it's only for a few subject that it doesn't work though...

I was wondering if anyone has add similar issues...

EDIT: Again, what for me is also very weird, is that if I start a project from scratch with the GUI (or if in the project I restart the preprocessing from the beginning), for the subject where R&U didn't work, it actually works if I process only only one session. So when done from the GUI it works. And I haven't extensively checked that every file is properly assigned... Getting a bit desperate at this point honestly.


Originally posted by Herberto Dhanis:
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?


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).

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Herberto Dhanis May 5, 2021
RE: Realignment & Unwarping fails for some subjects
Herberto Dhanis May 17, 2021