bids-standard / bids-validator

Validator for the Brain Imaging Data Structure
https://bids-standard.github.io/bids-validator/
MIT License
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`desc` keyword not allowed in toplevel derivatives dataset #1385

Open huy29433 opened 2 years ago

huy29433 commented 2 years ago

I want to create pipelines as derivatives of the Human Connectome dataset. Because I downloaded preprocessed files and for instance want to use the confounds, the toplevel is also a derivative dataset. However, it does not accept the desc keyword in _Human Connectome Project/sub-100206/sub-100206_task-wmdesc-confounds.tsv, which, in my opinion, is a mistake, as the specification states

desc Full name: Description

Format: desc-

Definition: When necessary to distinguish two files that do not otherwise have a distinguishing entity, the _desc-

This entity is only applicable to derivative data.

Here is my folder tree that throws the following error:

Error 1: [Code 1] NOT_INCLUDED

If I move the confounds file to a low-level derivatives folder, it does not throw an error.

Human Connectome Project
│   dataset_description.json
│   task-wm_run-1_bold.json
│
├───derivatives
│   └───MyPipeline
│       │
│       │   dataset_description.json
│       │
│       └───sub-100206
│
└───sub-100206
    │   sub-100206_task-wm_desc-confounds.tsv
    │
    └───func
            sub-100206_task-wm_run-1_bold.nii.gz
            sub-100206_task-wm_run-1_events.tsv

The following is the content of _Human Connectome Project/datasetdescription.json:

{
  "Name": "Human Connectome Project",
  "BIDSVersion": "1.6.0",
  "DatasetType": "derivative",
  "GeneratedBy": [
    {
      "Name": "Human Connectome Project"
    }
  ]
}
effigies commented 2 years ago

The validator does not yet support derivatives. Unfortunately it's been harder to find people with the necessary JavaScript skills and time to work on this, but we're currently working on setting up a dedicated sprint to bring the validator up to date with the spec.

huy29433 commented 2 years ago

I see, thank you very much for the quick answer!