How to handle subject who had to be taken out and put back in the scanner

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Hi all,

Forgive me if this is a newbie question :sweat_smile: I have a subject that completed about 1/2 of their task runs, but then had to be taken out of the scanner and put back in again. I did run another field map when they were put in the scanner again.

What is the best way to handle this in terms of using heudiconv to convert to BIDS and then running preprocessing with FMRIPREP? The study is meant to only be one session but for this subject, should I treat it as two sessions? I just want to ensure that the field maps get assigned to their correct runs and minimize headaches during analyses later on.

Thank you so much!

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Hi @krystalleger,

I can’t speak to the specifics of heudiconv; however, in this case you would treat this as a single session. According to the current BIDS spec:

However, for example, if a subject has to leave the scanner room and then be re-positioned on the scanner bed, the set of MRI acquisitions will still be considered as a session

Essentially, you’ll just need to ensure that the paths in the IntendedFor field of the 2nd field map(s) metadata map to the 2nd half functional task runs.

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