bids/validator repository overview

⁠BIDS-Validator

• BIDS-Validator⁠
  • Quickstart⁠
  • Support⁠
  • Maintainers and Contributors⁠
  • Use⁠
    • API⁠
    • .bidsignore⁠
    • Configuration⁠
    • In the Browser⁠
    • On the Server⁠
    • Through Command Line⁠
  • Docker image⁠
  • Python Library⁠
    • Example⁠
  • Development⁠
    • Running Locally in a Browser⁠
    • Testing⁠
    • Publishing⁠
  • Acknowledgments⁠

⁠Quickstart

1. Web version:
   1. Open Google Chrome⁠ or Mozilla Firefox⁠ (currently the only supported browsers)
   2. Go to http://bids-standard.github.io/bids-validator/⁠ and select a folder with your BIDS dataset. If the validator seems to be working longer than couple of minutes please open developer tools ⁠ and report the error at https://github.com/bids-standard/bids-validator/issues⁠.
2. Command line version:
   1. Install Node.js⁠ (at least version 10.11.0)
   2. Update npm to be at least version 7 (npm install --global npm@^7)
   3. From a terminal run npm install -g bids-validator
   4. Run bids-validator to start validating datasets.
3. Docker
   1. Install Docker
   2. From a terminal run docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data but replace the /path/to/data part of the command with your own path on your machine.
4. Python Library:
   1. Install Python⁠
   2. Install Pip⁠ package manager for Python, if not already installed.
   3. From a terminal run pip install bids_validator to acquire the BIDS Validator PyPi package⁠
   4. Open a Python terminal and type: python
   5. Import the BIDS Validator package from bids_validator import BIDSValidator
   6. Check if a file is BIDS compatible BIDSValidator().is_bids('path/to/a/bids/file')

⁠Support

The BIDS Validator is designed to work in both the browser and in Node.js. We target support for the latest long term stable (LTS) release of Node.js and the latest version of Chrome.

There is also a library of helper functions written in Python, for use with BIDS compliant applications written in this language.

Please report any issues you experience while using these support targets via the GitHub issue tracker⁠. If you experience issues outside of these supported environments and believe we should extend our targeted support feel free to open a new issue describing the issue, your support target and why you require extended support and we will address these issues on a case by case basis.

⁠Maintainers and Contributors

This project follows the all-contributors⁠ specification. Contributions of any kind are welcome!

The project is maintained by @rwblair⁠ with the help of many contributors listed below. (The emoji key⁠ is indicating the kind of contribution)

Please also see Acknowledgments⁠.

⁠Use

⁠API

The BIDS Validator has one primary method that takes a directory as either a path to the directory (node) or the object given by selecting a directory with a file input (browser), an options object, and a callback.

Available options include:

• ignoreWarnings - (boolean - defaults to false)
• ignoreNiftiHeaders - (boolean - defaults to false)

For example:

validate.BIDS(directory, {ignoreWarnings: true}, function (issues, summary) {console.log(issues.errors, issues.warnings);});

If you would like to test individual files you can use the file specific checks that we expose.

• validate.BIDS()
• validate.JSON()
• validate.TSV()
• validate.NIFTI()

Additionally you can reformat stored errors a