PHENOTYPE_SUBJECTS_MISSING issue

[JonteP]

Hello,

I've run into what might be an edge case. I have one participant with missing imaging data but questionnaires filled in. This participant is thus present in the phenotype folder and participants.tsv. This raises the error PHENOTYPE_SUBJECTS_MISSING when running the BIDS validator. Maybe there is something that I am missing, but it seems like the validator does not expect this scenario.

[sappelhoff]

Hi @JonteP, this may be of interest to you:

• Extra participants in phenotype TSVs, but not in data set folders should not be an ERROR in validation bids-specification#914

[effigies]

Is this an issue in the current (schema) validator?

[ericearl]

Yes. It is also causing errored validation on my old OpenNeuro dataset ds004215 (now ds005752). In our case there are 1,608 subjects with survey (phenotype/) data, but without sub-*/ directory data.

[effigies]

@ericearl My understanding is that this needs to be resolved in the specification (and schema). bids-standard/bids-specification#914 is where this needs to be finalized.

My reading is that we came to a position that seemed to work, and nobody objected, but a PR was never opened.

With the rule as written at the bottom, I don't think the expression language can express that rule yet, but we can figure that out.

[ericearl]

@effigies Cool, I will work on a PR to the spec now.

[ericearl]

PR added here: bids-standard/bids-specification#2044.