BIDS file naming convention when specifying runs

Hi,

I have a dataset where two pairs of spin echo field maps were collected (participants took a break in the middle of the scan). For a subset of participants however, the first pair of field maps are unusable because they contain the same phase encoding direction. In a fmap directory with both pairs I would name them as such:

sub-01_dir-AP_run-01_epi.json    
sub-01_dir-AP_run-01_epi.nii.gz  
sub-01_dir-AP_run-02_epi.json    
sub-01_dir-AP_run-02_epi.nii.gz
sub-01_dir-PA_run-01_epi.json
sub-01_dir-PA_run-01_epi.nii.gz
sub-01_dir-PA_run-02_epi.json
sub-01_dir-PA_run-02_epi.nii.gz

where run-01 refers to the first pair, and run-02 to the second pair.

For a participant with only 1 good pair of field maps, should I still specify the run tag (for naming consistency sake across the dataset), or not (for parsimony sake)? I’m leaning towards the latter, since run is an optional tag and there aren’t multiple acquisitions with the same parameters, but I wanted to check before proceeding.

Thanks for the help.

Either would be fine, as far as BIDS is concerned. I don’t personally have a strong feeling either way, but it might be worth noting in the README.

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