bids-standard / bids-2-devel

Discussions and suggestions of backwards incompatible changes to BIDS
https://bids.neuroimaging.io/
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_mod entity: should it be kept, dissolved, transformed, or embraced? #70

Open yarikoptic opened 2 months ago

yarikoptic commented 2 months ago

_mod was introduced and is used primarily to disambiguate different _defacemasks. So, to a degree, it encapsulates the semantic that some, but not all, _suffixes correspond to MRI modalities (really) as a summarized in a comment to #58.

It is only present only when there is a _defacemask and only for anat/, while in effect most of the time corresponding to those suffixes "implicitly" where suffix does correspond to "contrast" (not modality really).

Samples from openneuro ```shell $> for ds in ds*; do f=$(find $ds -iname *_mod-* | head -n 1); [ -z "$f" ] && continue; echo "$f"; done ds000113/sub-01/ses-forrestgump/anat/sub-01_ses-forrestgump_acq-mag_mod-veno_defacemask.nii.gz ds000224/sub-MSC01/ses-struct01/anat/sub-MSC01_ses-struct01_run-01_mod-T1w_defacemask.nii.gz ds000233/sub-rid000001/anat/sub-rid000001_mod-T1w_defacemask.nii.gz ds001297/sub-01/anat/sub-01_acq-filt_mod-T1w_defacemask.nii.gz ds002718/sub-002/anat/sub-002_mod-T1w_defacemask.nii.gz ds003645/sub-002/anat/sub-002_mod-T1w_defacemask.nii.gz ds004192/sub-01/ses-localizer1/anat/sub-01_ses-localizer1_acq-prescannormalized_rec-pydeface_mod-T1w_defacemask.nii.gz ds004712/sub-03286/ses-NOT1ACH001/anat/sub-03286_ses-NOT1ACH001_mod-T1w_defacemask.nii.gz ```

Also there is

where the point of having _mod is coming up. And as we are planing to proceed with

if we get an entity _mod which actually corresponds to modality (mri, eeg, ...) not just mere contrast, it somewhat makes it then explicit and consistent to then "embrace" that entity and use it consistently to disambiguate all files, not just _defacemasks.

Note: if to be kept just for the sake of disambiguation of some _suffix2 (e.g. _defacemask) among different _suffixes (e.g. _T1w and _T2w) as it is now, yet another use is _events.tsv files which came up in the context of

Remi-Gau commented 2 months ago