qMRI JSON not allowed in root of dataset

[Remi-Gau]

Noticed on one of my own dataset but tried the following on the bids example repo to demonstrate

cp qmri_mp2rage/sub-1/anat/sub-1_inv-1_MP2RAGE.json qmri_mp2rage/inv-1_MP2RAGE.json

tree qmri_mp2rage

qmri_mp2rage
├── dataset_description.json
├── derivatives
├── inv-1_MP2RAGE.json           #  <---- this should be valid, no?
├── README
└── sub-1
    └── anat
        ├── sub-1_inv-1_MP2RAGE.json
        ├── sub-1_inv-1_part-mag_MP2RAGE.nii
        ├── sub-1_inv-1_part-phase_MP2RAGE.nii
        ├── sub-1_inv-2_MP2RAGE.json
        ├── sub-1_inv-2_part-mag_MP2RAGE.nii
        ├── sub-1_inv-2_part-phase_MP2RAGE.nii
        └── sub-1_mod-MP2RAGE_defacemask.nii.gz

bids-validator qmri_mp2rage

[email protected]
bids-specification@disable
        1: [ERR] Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder. (code: 1 - NOT_INCLUDED)
                ./inv-1_MP2RAGE.json
                        Evidence: inv-1_MP2RAGE.json

Was getting a similar error for UNIT1.json in the root folder of the dataset. I have not checked other qMRI related suffixes.

@agahkarakuzu Can you cross check if you have time?

[Remi-Gau]

Any news on this? Can I help in any way?

[sappelhoff]

it's possible that all that's needed is an edit of https://github.com/bids-standard/bids-validator/blob/master/bids-validator/bids_validator/rules/top_level_rules.json -- so I think if you are keen, you could look into that?

[Remi-Gau]

Thanks that helps as a pointer as to where to start!

Will look into it but writing regular expression for qMRI files defo sounds fun... #KMN

Should be tweak the bids example so that we have sort of test for this?

[sappelhoff]

@Remi-Gau can this issue now that #1546 has been merged be closed ?

[Remi-Gau]

Yup