Anatomical Image Filenames in BIDS? (Two images have same scanning parameters, but different slices)

1

Hello NeuroStars!

I’m getting some data organized into BIDS format for a new study in which data collection is ongoing. As part of our protocol, we are collecting two high-resolution anatomical images. They have the same exact scanning parameters, but one is collected with a field of view that is more superior. The idea is that the two scans are imaging two separate brainstem nuclei (locus coeruleus and substantia nigra).

Right now we are naming the files like so:
sub-SUBJECT_ses-SESSION_run-01_mt-on_TSE.nii.gz

I thought about just adjusting the ‘run’ entity (e.g. locus coeruleus scan is run-01, and substantia nigra scan is run-02) but sometimes we acquire multiple runs of a single scan if it seems like there might be an artifact or motion.

I’m wondering if there’s a good entity for differentiating the two fields of view. I’m not really seeing anything in the specification here: Magnetic Resonance Imaging - Brain Imaging Data Structure v1.8.0

Thanks!

  • Tom
2

Hi @tmorin01,

You can use the acq-<>label.

sub-XX_ses-XX_acq-LC/SN_mt-on_<suffix>.nii.gz

Where LC and SN could indicate your two nuclei, for example. Just make sure to include in your BIDS README file a description of what LC/SN (or whatever label you choose) are.

However, TSE is not a valid suffix. The only valid suffixes for files that use the mt-<> label are MPM, MTS, MTR.

Best,
Steven