Support latest version of the BIDS specifications

[NicolasGensollen]

The current version of the BIDS specifications is 1.9.0 and was released in November 2023:

https://bids-specification.readthedocs.io/en/stable/CHANGES.html

The version that Clinica currently officially support is 1.7.0:

clinica/clinica/utils/bids.py

Line 15 in e2c421c

BIDS_VERSION = "1.7.0"

Which was released back in February 2022.

We should investigate to see whether we need to make some changes to the code in order to be compliant with the latest version of the specifications.

• adni-to-bids
• aibl-to-bids
• genfi-to-bids
• habs-to-bids
• ixi-to-bids (See [CONV] IXI-to-BIDS modifications to fit BIDS specifications 1.10  #1310 )
• nifd-to-bids
• oasis-to-bids
• oasis3-to-bids
• ukb-to-bids

[NicolasGensollen]

Actually the 1.10.0 release of the specifications was released three days ago: https://github.com/bids-standard/bids-specification/releases

[NicolasGensollen]

Moved this to the 0.10.0 milestone as there is some work to do to ensure full BIDS compliance.

Here is a temporary list from @AliceJoubert :

• See if and how we can add the bids-validator to our CI for the outputs of the converters
• Check our CI data
• Handle compatibility issues between converter outputs and BIDS specifications:

1. Missing JSON files for PET scans (adni-to-bids, nifd-to-bids)
2. Missing keys in JSON files for PET scans (aibl-to-bids, oasis3-to-bids, habs-to-bids)
3. Missing keys in JSON files for func (adni-to-bids, genfi-to-bids, ukb-to-bids)
4. Missing b files for DWI (genfi-to-bids, ixi-to-bids)
5. Issues in TSV format (adni-to-bids, aibl-to-bids, genfi-to-bids, ixi-to-bids)

[github-actions]

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