Specifying run number(s) in BIDS

1

I’ve generally viewed the _run- label as an optional field except for func acquisitions. I realize that the BIDS specification contains this important line regarding runs

If several scans of the same modality are acquired they MUST be indexed with the run-<index> key-value pair: _run-1 , _run-2 , _run-3 , and so on (only nonnegative integers are allowed as run labels).

which leads me to a couple case-scenario questions:

1). If I were to collect two separate anat/T1w acquisitions, but the parameters were different and noted in the _acq-, _desc-, _ce-, or some other label, would the run label still be necessary for these two?

2). If I collect four dwi/dwi acquisitions (two AP, two PA), do the run numbers need to go 01-04, or is this appropriate:

sub_01_dir-AP_run-01_dwi.nii.gz
sub_01_dir-PA_run-01_dwi.nii.gz
sub_01_dir-AP_run-02_dwi.nii.gz
sub_01_dir-PA_run-02_dwi.nii.gz

My impression is that BIDS doesn’t particularly care, but I’m curious if there’s some preferred method?

Thank!

2

  1. No, run- is intended to be runs that are essentially identical. Changing acq-, desc- or ce- indicates a different set of parameters, so you only need to add run- if you have multiple files where the other entities are the same.

  2. What you’ve shown is fine.

Feel free to open a PR against the spec to make the language clearer.

3

Sure, I’ll submit a PR sometime next week

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