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BIDS validation

The BIDS Validator is a tool that checks if a dataset is compliant with the BIDS standard. The validator is available for use within several different environments to best suit individual user preferences and use cases, those versions are:

Instructions to install and use these versions can be found within the quickstart guide at the BIDS Validator repository.

Note

For more information about the development of the validator, check this blog post about it.

Data Privacy and Confidentiality

Please note that the web app is entirely browser (not server) based. As such, there is no file uploading as part of the validation.

Browser Version

  1. The BIDS Validator can be found at http://bids-standard.github.io/bids-validator/. It requires that you use the Chrome or Firefox browser, since those are the only ones in which you can select a whole folder rather than individual files.

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  2. You can then choose the folder that you wish to validate

Types of Feedback

Error

This response indicates that your dataset is not BIDS compliant. Try following the suggestions listed to make the appropriate corrections.

Error

Warning

This response indicates that your dataset is BIDS compliant, but there are some non-critical problems (such as recommended fields missing, or differences between participants).

Warning

Success 🚀

This response indicates that your folder contains a valid BIDS Dataset!

Command Line Version

Verifying a BIDS compliant data set

After installation with deno using the CLI is relatively simple. Locate a bids data set similar to the one below:

user@host:~/bids-examples$ tree pet001

sub001/
├── dataset_description.json
├── participants.json
├── participants.tsv
├── README
└── sub-01
    └── ses-01
        ├── anat
        │   ├── sub-01_ses-01_T1w.json
        │   └── sub-01_ses-01_T1w.nii
        └── pet
            ├── sub-01_ses-01_trc-CIMBI36_pet.json
            ├── sub-01_ses-01_trc-CIMBI36_pet.nii.gz
            ├── sub-01_ses-01_trc-CIMBI36_recording-autosampler_blood.json
            ├── sub-01_ses-01_trc-CIMBI36_recording-autosampler_blood.tsv
            ├── sub-01_ses-01_trc-CIMBI36_recording-manual_blood.json
            └── sub-01_ses-01_trc-CIMBI36_recording-manual_blood.tsv

Now simply point the bids validator at the folder path of the subject(s) in question:

user@host:~/bids-examples$ bids-validator pet001

Types of Feedback

Error

As is the case with the browser or any version of the validator follow the [ERROR] messages and correct until bids-validator returns 0 errors after running.

[ERROR] NIFTI_HEADER_UNREADABLE We were unable to parse header data from this NIfTI file. Please ensure it is not corrupted or mislabeled.
            /sub-01/ses-01/anat/sub-01_ses-01_T1w.nii

    Please visit https://neurostars.org/search?q=NIFTI_HEADER_UNREADABLE for existing conversations about this issue.

Warning

As stated with the browser version above, one may elect to ignore warnings, but the information provided via the validator should help to pinpoint where and how to resolve some of these warnings. When in doubt consult the BIDS specification

[WARNING] JSON_KEY_RECOMMENDED A JSON file is missing a key listed as recommended.
            DatasetType
            /dataset_description.json

            GeneratedBy
            /dataset_description.json

            SourceDatasets
            /dataset_description.json

    Please visit https://neurostars.org/search?q=JSON_KEY_RECOMMENDED for existing conversations about this issue.

Success 🚀

Pass go and collect 200 dollars, the data set in question passes validation.

user@host:~/bids-examples$ bids-validator sub001

      Summary:                         Available Tasks:        Available Modalities:
      12 Files, 224 kB                                         PET
      1 - Subjects 1 - Sessions                                MRI

    If you have any questions, please post on https://neurostars.org/tags/bids.