Mutiple fmap files in one session - proper set up


I have decided to start using fMRIprep and I am setting up my data according to the BIDS format. However, I am a bit confused on how to deal with a couple of scenarios. Mostly because I probably don’t have a clear understanding of what will happen down the road (I’ve searched the board for similar issues and I could only find partial answers).

Scan session description:
participants come only “once” and perform several func tasks, a T1w (MPRAGE), a fMAP, and a DWI (pseudo randomized order).

The typical structure is:

  • Raw/
    • anat/
    • beh/
    • dwi/
    • fmap/
    • func/

However, in some situations the participant came out of the scan and they have a second fMap. In other scenarios, participants did not complete all the tasks and had to return a week later to finish up. In this case we have both a new MPRAGE and a new fMAP.

What is the proper way for naming these additional scans. Does the change in name for these particular participants affect the naming of all participants?

I am using dcm2bids to create my nii.gz and json files. For now, I’ve exported the scans separately (the fMAP with only the few func scans to which it applied) and saved them with a temporary sub number (e.g., sub-001 for the first set of tasks with the first fmap, and sub-901 for the remaining tasks and the second fmap). Note, my config files for dcm2bids are very bare bones.

I’m sure these are pretty common scenarios and would really appreciate expert user’s solutions.

Thank you in advance for your time (I’m still new to the fMRIprep environment and the dcm2bids process, your patience is appreciated).


Hi Ilaria,

I do not believe that _fmap is a valid suffix for fieldmaps. Depending on the kind of acquisition it will be typically (1) magnitude.nii.gz/json paired with a _phasediff.nii.gz/json, (2) epi.nii.gz/.json, or (3) _fieldmap.nii.gz/.json paired with a magnitude.nii.gz/.json file. See more here.

You should make sure your data are bids valid with the BIDS validator.

There are two ways to address this. One would be to code this by ses- labels (so you can have one for ses-orig and one for ses-makeup. Another would be to add something like an acq-makeup field for the extra images. Both are technically BIDS valid, and what works best for you may depend on your analyses workflows.

Depends. If you go the session route, then you will probably want all subjects to atleast have a ses-orig, just to make the coding easier down the line. If you go the acq route, then you wouldn’t necessarily need to change the filenames for other participants.

Just make sure the IntendedFor fields in the fmap json files map to the correct images to be applied to!

Hope this helps,

Hello Steven,

thank you very much for answering my questions and for correcting my file naming.
I am assuming that the folder name fmap/ is accurate and I need to fix the suffix for the file.

Because I’ve already exported most of my participants, I think I’ll go with the acq-makeup field.
Sorry for the additional basic questions:

  • may I simply rename my _fieldmap.nii.gz files or must I export them again and make sure that my config file in dcm2bids has the new name for the makeup fmap?
  • and a follow up: if I need to export again the files, should I be exporting all the files from a scan session together or may I just export the makeup files and their corresponding func scans?

thank you again for your time and patience.

You could simply rename the files, but changing the dcm2bids file may also be helpful incase you need 1) rexport everything, 2) share DICOMS, 3) prepare BIDS formats for similar acquisitions your lab uses.

As long as you’re using the same dcm2niix and dcm2bids version, I think you should be okay just exporting the files that are not currently in your BIDS root directory.

Thank you so much for your help!
Have a lovely rest of the day.