Using the command line

Using the command line#

The BIDS Validator may be run with the Deno runtime. For detailed installation instructions, see Deno - Installation. Deno is also available as a conda-forge package.

Installation#

In general, there is no need to install Deno applications. deno run allows running from the Javascript Repository:

deno run -ERWN jsr:@bids/validator <dataset>

However, you can also install a lightweight script (into $HOME/.deno/bin):

deno install -ERWN -g -n bids-validator jsr:@bids/validator

Or compile a bundled binary:

deno compile -ERWN -o bids-validator jsr:@bids/validator

Usage#

The BIDS Validator takes a single dataset as input:

deno run -ERWN jsr:@bids/validator <dataset>

bids-validator <dataset>

Options#

Option

Description

-v, --verbose

Log more extensive information about issues

-s URL, --schema URL

Specify an alternative BIDS Schema for validation

-c FILE, --config FILE

Provide a configuration file

-r, --recursive

Validate datasets found in derivatives/ subdirectories, recursively

-p, --prune

Prune derivatives and sourcedata directories on load (disables -r and will underestimate dataset size). This can speed up validation of large datasets.

-o FILE, --outfile FILE

Write validation results to file.

--format

Output format. One of text (default), json, or json_pp (pretty-printed JSON)

--json

Shorthand for --format json

--ignoreWarnings

Do not report warnings

--ignoreNiftiHeaders

Do not open NIfTI files, skipping any checks that rely on NIfTI header data

--filenameMode

Perform filename checks only on newline-separated filenames read from stdin

--blacklistModalities MOD...

Raise error if passed modalities are detected in the dataset. Modalities may be any of mri, eeg, ieeg, meg, beh, pet, micr, motion, nirs, or mrs.

--datasetTypes TYPE...

Permitted dataset types to validate against (default: all). Types may be any of raw, derivative, study.

--debug LEVEL

Enable logging at the specified level. Default level is ERROR. Levels include (from most to least verbose): NOTSET, DEBUG, INFO, WARN, ERROR, CRITICAL.

--color, --no-color

Enable/disable color. The validator also respects the NO_COLOR and FORCE_COLOR environment variables.

--preferredRemote

Name of the preferred git-annex remote for accessing remote data. This is experimental. The default is to use the most recently created S3 remote.

--git-ref [REF]

Validate files from a git tree instead of the filesystem. REF may be a branch, tag, or (abbreviated) commit SHA; defaults to HEAD when omitted. Useful for validating a dataset without a working tree checkout. Combine with --preferredRemote to select a git-annex remote for annexed content.

Configuration file#

The schema validator accepts a JSON configuration file that reclassifies issues as warnings, errors or ignored.

{
  "ignore": [
    { "code": "JSON_KEY_RECOMMENDED", "location": "/T1w.json" }
  ],
  "warning": [],
  "error": [
    { "code": "NO_AUTHORS" }
  ]
}

When a configuration specifies location without leading / it is interpreted as a glob pattern following gitignore syntax. The issues are partial matches of the Issues that the validator accumulates. Pass the --json flag to see the issues in detail.

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