Subject Taken Out of Scanner - How to Put in BIDS Format

Hi,
I have a subject who completed about half of their runs before needing to be taken out of the fMRI scanner. They later completed the session, but now I have two sets of field map scans, each corresponding to different functional runs. How do I organize the data in such a way that it is clear which field map scans correspond to which set of runs? BIDS documentation seems to very briefly touch on this, saying I should put them all in the same session (instead of breaking up the sessions when the subject left the scanner), but I haven’t found anything to address the two sets of field maps. I appreciate your help and time!
Best,
Ben

If I understand you correctly, you have a session that was essentially split in parts, e.g., for a four run session, runs 1 and 2 were collected in succession, the subject was taken out, and runs 3 and 4 were collected in succession.

sub-01/
  func/
    sub-01_task-task_run-1_bold.nii.gz
    sub-01_task-task_run-2_bold.nii.gz
    sub-01_task-task_run-3_bold.nii.gz
    sub-01_task-task_run-4_bold.nii.gz

Because the subject would not be aligned, a new fieldmap was taken in the second group, so you have two (let’s assume) fieldmap.nii.gz files. In this case, I would break up the fieldmaps by run:

sub-01/fmap/sub-01_run-1_fieldmap.nii.gz
sub-01/fmap/sub-01_run-2_fieldmap.nii.gz

Then to specify which fieldmaps apply to which BOLD series, you would use the IntendedFor metadata in the JSON sidecars:

  • sub-01/fmap/sub-01_run-1_fieldmap.json:

    {"IntendedFor": [
       "func/sub-01_task-task_run-1_bold.nii.gz",
       "func/sub-01_task-task_run-2_bold.nii.gz"]
    }
    
  • sub-01/fmap/sub-01_run-2_fieldmap.json:

    {"IntendedFor": [
       "func/sub-01_task-task_run-3_bold.nii.gz",
       "func/sub-01_task-task_run-4_bold.nii.gz"]
    }
    

Does that answer your question?

Hi,
Great, thank you very much for your response and answer. Very helpful. You understood the question exactly right. Just for complete clarity, I believe inside the “IntendedFor” for the first field map run you mean “…_run-1_bold…” and “…_run-2_bold…”, not run-1 twice, correct? And when I use dcm2niix to convert the dicoms, the “IntendedFor” field is not automatically made. So I will make the “IntendedFor” for this subject in question, but do you also recommend I make it for every other subject and session too? Even after including the “IntendedFor”, will BIDS-apps be able to pick up on which field maps are intended for which scans or can I expect to have to deal with this issue in later analyses?
Thank you!
Ben

I believe inside the “IntendedFor” for the first field map run you mean “…_run-1_bold…” and “…_run-2_bold…”, not run-1 twice, correct?

That’s correct. I suspect this was a typo.

So I will make the “IntendedFor” for this subject in question, but do you also recommend I make it for every other subject and session too?

Yes you need that field in the json of every fieldmap and this is definitely something you need to create manually: not sure if there are some “smart” converters out there where you input that info in and it creates the json files for you.

Note to self (feel free to ignore): not sure if there is a way to use the “inheritance principle” on the json of the fieldmaps in this case. Would they be in the root folder and just called run-1_fieldmap.json? that looks weird to me.

Good catch, fixed.

+1 to everything @Remi-Gau said. In general, fieldmaps need IntendedFor. (Note that https://github.com/bids-standard/bids-specification/pull/622 is intended to permit additional use cases, but you should still use IntendedFor when your use case fits.)

You can use the inheritance principle for describing the sequence but not IntendedFor. I am skeptical that any savings in verbosity would be worth the complication of resolving the meaning unambiguously.