Error on physio data in anat sub-directory

[tstoeter]

While conducting our multi-modal MRI study, also a physiological baseline (cardiac and respiratory) was acquired parallel to the anatomical measurements. According to the BIDS specifications on physiological recordings (https://bids-specification.readthedocs.io/en/latest/modality-specific-files/physiological-recordings.html), the physio data files (.tsv.gz and .json) may be stored in the subject's anatomical recordings sub-directory. We have T1w and PDw anatomical recordings and corresponding physio data only for the T1w recording. The subject directories currently look as follows:

...
./physio.json
./sub-01/
./sub-01/anat/
./sub-01/anat/sub-01_PDw.nii.gz
./sub-01/anat/sub-01_T1w.nii.gz
./sub-01/anat/sub-01_T1w.json
./sub-01/anat/sub-01_PDw.json
./sub-01/anat/sub-01_physio.tsv.gz
...

The specification's naming convention for physio data within modality sub-directories is:

<matches>[_recording-<label>]_physio.tsv.gz
<matches>[_recording-<label>]_physio.json

Therefore, in the example above, the part <matches> is sub-01, [_recording-<label>] is empty (we only have one physio recording), and the modality suffix is _physio. Hence, we have sub-01_physio.tsv.gz as the filename. Now, we are facing two problems.

1. With this naming scheme we cannot relate the physio data to the T1w recording from the filename. Is there an alternative way to capture this relationship?
2. The bids-validator (bids-validator@1.14.14 and also 1.14.15-dev) complains with an error about this naming scheme.

1: [ERR] Files with such naming scheme are not part of BIDS specification. ... (code: 1 - NOT_INCLUDED)
		./sub-01/anat/sub-01_physio.tsv.gz
			Evidence: sub-01_physio.tsv.gz

I had a look at the source code bids-validator/bids_validator/rules/file_level_rules.json. For EEG, *_physio.tsv.gz seems to be covered:

      "@@@_cont_ext_@@@": [
        "_physio\\.tsv\\.gz",
        "_stim\\.tsv\\.gz",
        "_physio\\.json",
        "_stim\\.json"
      ]

However, there is no such block for "anat_nonparametric" (where we have T1w and PDw suffixes) in this rules file. Is this the issue for why the bids-validator complains? I'm happy to provide a PR, if this is the correct place to fix it.

[rwblair]

Looks like this is an issue in both the node and deno versions of the validator.

The node version validates filenames using the regex in the bids-validator/bids_validator/rules/ as you showed. I went ahead and made a PR for it. #2165

The deno version validates file names using the schema in the bids-specification itself. I'm still working on a PR for the specification to fix this.

[effigies]

It looks like bids-standard/bids-specification#513 explicitly permitted it for anat, but the naming convention was not clarified for datatypes that permit unrelated scans that are distinguished only by suffix (which I think is only anat...).

I guess I would say you could use acq-T1w_physio.nii.gz to indicate that it corresponds to a T1w scan. The mod- entity would seem to be applicable here, but that would require an addition to the specification to actually say that it can be used.

[tstoeter]

Thank you very much @rwblair and @effigies for fixing our issues so quickly! I tested the latest version with file names sub-01_physio.tsv.gz, as well as sub-01_acq-T1w_physio.tsv.gz. In both cases, the validator passed without error. We will stick with acq-T1w for making the relation clear. Thank you @effigies for pointing it out!

[tstoeter]

We tried uploading our dataset to OpenNeuro, but were faced with two validation errors. I realized I had used the legacy validator before, and OpenNeuro uses the new deno based validator. I could resolve one issue, but not this one:

ERROR: ALL_FILENAME_RULES_HAVE_ISSUES

Multiple filename rules were found as potential matches. All of them had at least one issue during filename validation.

    /sub-11/anat/sub-11_acq-T1w_physio.tsv.gz (Rules that matched with issues: rules.files.raw.task.timeseries, rules.files.raw.task.timeseries__mri_no_task, rules.files.raw.task.timeseries__func, rules.files.raw.task.timeseries__meg, rules.files.raw.task.timeseries__motion)

We do not get this one with the legacy validator version 1.15. Is this naming scheme, that was newly supported by the patches above, not yet covered in the deno based validator?