Can I use head localisers to inform the registration of fMRI into the T1w scan in fMRIprep


I have an experiment where some participants are taking a break in the middle of the scan and a new head localiser is retrieved. Is there a way that I can use the head localisers that are taken by the scan each time to inform on the registration of the fMRI sequences into the T1w scan during preprocessing with fMRIprep?

Thank you

I do not believe this is possible.


Thank you again for your reply in yet another post. Given that I have separate fieldmaps for each part (before and after the break) could I use separate fieldmaps for each part of the session when using fMRIprep (as an alternative)?

Really appreciate your input thus far.



Yes. In the field map json files, you can set or add the “IntendedFor” field to associate a field map with a functional scan.

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