Bids-validator vs BIDS Specification for T2starw

sslevinski · December 14, 2023, 8:22pm

I’m trying to validate a BIDS dataset and I’m getting an error that the T2starw files are NOT_INCLUDED.

The reason seems to be that the BIDS Specification allows for echo with T2Starw but the bids-validator does not. I guess this would be true for all non-parametric structural MR images.

Example file:
rawdata/sub-142/ses-60238918/anat/sub-142_ses-60238918_acq-T2MAPGRE_echo-0_T2starw.nii.gz

bids-validator regexp for T2starw does not allow for “echo”

github.com

bids-standard/bids-validator/blob/1163824c837910ba6ceebc38e3098438221f8bf1/bids-validator/bids_validator/rules/file_level_rules.json#L9


      
          {
            "anat_nonparametric": {
              "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?anat[\\/\\\\]\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_ce-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_part-(imag|mag|phase|real))?_(?:@@@_anat_suffixes_@@@)\\.(@@@_anat_ext_@@@)$",
              "tokens": {
                "@@@_anat_suffixes_@@@": [
                  "T1w",
                  "T2w",
                  "PDw",
                  "T2starw",
                  "FLAIR",
                  "inplaneT1",
                  "inplaneT2",
                  "PDT2",
                  "angio",
                  "T2star",
                  "FLASH",
                  "PD"
                ],
                "@@@_anat_ext_@@@": ["nii\\.gz", "nii", "json"]

BIDS Specification for T2starw does allow for “echo” in both the Modality specific files section and the Entity Table appendix.
https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetic-resonance-imaging-data.html#non-parametric-structural-mr-images
https://bids-specification.readthedocs.io/en/stable/appendices/entity-table.html

The easy solution seems to be to change the “echo” to “run” and bump the index up by 1.

Thoughts or opinions?

I guess I could also create an issue with the bids-validator or modify the offending bids-validator file and submit a patch.

effigies · December 14, 2023, 8:29pm

Please do. If the spec allows it and the validator doesn’t, that’s a bug and should be handled on the issue tracker.

sslevinski · December 14, 2023, 8:43pm

I have entered an issue on github. I also noticed that chunk should be allowed as well.

github.com/bids-standard/bids-validator

BIDS Specification is different than bids-validator for non-parametric structural MR images

opened 08:42PM - 14 Dec 23 UTC

Slevinski

The BIDS Specification allows for **echo** and **chunk** with non-parametric str…uctural MR images. The bids-validator does not. **bids-validator** https://github.com/bids-standard/bids-validator/blob/1163824c837910ba6ceebc38e3098438221f8bf1/bids-validator/bids_validator/rules/file_level_rules.json#L3 **BIDS Specification** Modality specific files section and the Entity Table appendix. https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetic-resonance-imaging-data.html#non-parametric-structural-mr-images https://bids-specification.readthedocs.io/en/stable/appendices/entity-table.html For the bids-validator, the new line should be: "regexp": "^[\\/\\\\](sub-[a-zA-Z0-9]+)[\\/\\\\](?:(ses-[a-zA-Z0-9]+)[\\/\\\\])?anat[\\/\\\\]\\1(_\\2)?(?:_task-[a-zA-Z0-9]+)?(?:_acq-[a-zA-Z0-9]+)?(?:_ce-[a-zA-Z0-9]+)?(?:_rec-[a-zA-Z0-9]+)?(?:_run-[0-9]+)?(?:_echo-[0-9]+)?(?:_part-(imag|mag|phase|real))?(?:_chunk-[0-9]+)?_(?:@@@_anat_suffixes_@@@)\\.(@@@_anat_ext_@@@)$",

sslevinski · December 14, 2023, 10:05pm

Also create pull request with the fix.