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[FIX] use bids uri for qmri derivatives #339

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Remi-Gau
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fixes #312

@sappelhoff does that make sense as a way to refer to source data in the derivatives using bids uri?

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Co-authored-by: Stefan Appelhoff <[email protected]>
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effigies commented Nov 8, 2022

I could swear we had a conversation where we dropped the file:// for relative paths. That's not a universal interpretation of file:///

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effigies commented Nov 8, 2022

Oh, I see. That predates the BIDS URI discussion altogether. I would still use plain relative paths. Note in Examples we use relative paths (no file://), absolute paths (with file:///) and external URIs.

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mh then we have two ways of specifying relative paths in the spec, should we clarify that?

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Remi-Gau commented Nov 8, 2022

mh then we have two ways of specifying relative paths in the spec, should we clarify that?

yes please. 😝

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I think we are safe dropping the file:// here, so my earlier recommendation was wrong (sorry).

I have opened a discussion here:

qmri_mpm/derivatives/hmri/dataset_description.json Outdated Show resolved Hide resolved
qmri_mtsat/derivatives/qMRLab/dataset_description.json Outdated Show resolved Hide resolved
qmri_vfa/derivatives/qMRLab/dataset_description.json Outdated Show resolved Hide resolved
Co-authored-by: Stefan Appelhoff <[email protected]>
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Changes here look good to me @Remi-Gau except for that one comment above. Once that is resolved, I think we can merge and mirror the change to the upstream (real) data

"sub-01/fmap/sub-01_flip-01_TB1DAM.nii.gz",
"sub-01/fmap/sub-01_flip-02_TB1DAM.nii.gz"
"bids:source:sub-01/sub-01/fmap/sub-01_flip-01_TB1DAM.nii.gz",
"bids:source:sub-01/sub-01/fmap/sub-01_flip-02_TB1DAM.nii.gz"
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I think RawSources does not permit BIDS URIs, only dataset relative links. Also, that field is deprecated in favor of Sources (which does permit BIDS URIs)

https://bids-specification.readthedocs.io/en/latest/glossary.html#rawsources-metadata

I think we should either just use relative links here, OR turn the RawSources here into Sources

@sappelhoff sappelhoff added this to the 1.9.0 milestone Mar 19, 2023
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MPM fmap in derivatives are intended for data in the raw dataset
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