/bids-validator

Validator for the Brain Imaging Data Structure

Primary LanguageJavaScriptMIT LicenseMIT

CircleCI Gitlab pipeline status Codecov DOI

BIDS-Validator

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 12.12.0)
    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

All 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.


Adam Li
💻 ⚠️ 📓 🐛
Adam Thomas
📖
Alexander Jones
💻 ⚠️ 🤔
Chris Gorgolewski
🐛 💻 🔣 📖 💡 🤔 🚇 🚧 🧑‍🏫 💬 👀 ⚠️ ✅ 📢 📓
Chris Holdgraf
💻
Chris Markiewicz
💻 ⚠️ 🤔 🐛 💬 🔧 🚧
David Nishikawa
💻 ⚠️

Dimitri Papadopoulos Orfanos
💻
Duncan Macleod
🚇
Franklin Feingold
📖
Gregory noack
💻 ⚠️
Horea Christian
💻
Jakub Kaczmarzyk
🚇
Joke Durnez
💻

Mainak Jas
💻 ⚠️ 🤔 👀 📓
Marco Castellaro
💻 ⚠️
Max
💻 🐛
Michael Hanke
📖
Mikael Naveau
💻
Nell Hardcastle
💻 🤔 🚇 💬 👀
Nicolas Traut
💻

Parul Sethi
💻 ⚠️
Patricia Clement
💻
Remi Gau
💻 📖 📓
Richard Höchenberger
💻 📓 ⚠️ 🐛
Robert Oostenveld
💻 🤔 🐛 ⚠️
Rohan Goyal
💻
Ross Blair
🚧 🤔 💻 🐛 🚇 📆 💬 👀 🔧 ⚠️

Russ Poldrack
💻 💵 🔍
Soichi Hayashi
🐛
Stefan Appelhoff
🐛 💻 🔣 📖 💡 🤔 🚇 🚧 🧑‍🏫 💬 👀 ⚠️ ✅ 📢 📓
Suyash
💻
Taylor Salo
💻
Teal Hobson-Lowther
💻 ⚠️
Travis Riddle
🐛

VisLab
🤔 💻
Wazeer Zulfikar
📖
Yaroslav Halchenko
🤔 💻 📖 📓
constellates
💻 ⚠️
dewarrn1
💻
dkp
💻
goldmund
💻 ⚠️

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 against a new config using validate.reformat()

.bidsignore

Optionally one can include a .bidsignore file in the root of the dataset. This file lists patterns (compatible with the .gitignore syntax) defining files that should be ignored by the validator. This option is useful when the validated dataset includes file types not yet supported by BIDS specification.

*_not_bids.txt
extra_data/

Configuration

You can configure the severity of errors by passing a json configuration file with a -c or --config flag to the command line interface or by defining a config object on the options object passed during javascript usage.

If no path is specified a default path of .bids-validator-config.json will be used. You can add this file to your dataset to share dataset specific validation configuration. To disable this behavior use --no-config and the default configuration will be used.

The basic configuration format is outlined below. All configuration is optional.

{
	"ignore": [],
	"warn": [],
	"error": [],
	"ignoredFiles": []
}

ignoredFiles takes a list of file paths or glob patterns you'd like to ignore. Lets say we want to ignore all files and sub-directory under /derivatives/. This is not the same syntax as used in the .bidsignore file

{
	"ignoredFiles": ["/derivatives/**"]
}

Note that adding two stars ** in path makes validator recognize all files and sub-dir to be ignored.

ignore, warn, and error take lists of issue codes or issue keys and change the severity of those issues so they are either ignored or reported as warnings or errors. You can find a list of all available issues at utils/issues/list.

Some issues may be ignored by default, but can be elevated to warnings or errors. These provide a way to check for common things that are more specific than BIDS compatibility. An example is a check for the presence of a T1w modality. The following would raise an error if no T1W image was found in a dataset.

{
	"error": ["NO_T1W"]
}

In addition to issue codes and keys these lists can also contain objects with and "and" or "or" properties set to arrays of codes or keys. These allow some level of conditional logic when configuring issues. For example:

{
	"ignore": [
		{
			"and": [
				"ECHO_TIME_GREATER_THAN",
				"ECHO_TIME_NOT_DEFINED"
			]
		}
	]
}

In the above example the two issues will only be ignored if both of them are triggered during validation.

{
	"ignore": [
		{
			"and": [
				"ECHO_TIME_GREATER_THAN",
				"ECHO_TIME_NOT_DEFINED"
				{
					"or": [
						"ECHO_TIME1-2_NOT_DEFINED",
						"ECHO_TIME_MUST_DEFINE"
					]
				}
			]
		}
	]
}

And in this example the listed issues will only be ignored if ECHO_TIME_GREATER_THAN, ECHO_TIME_NOT_DEFINED and either ECHO_TIME1-2_NOT_DEFINED or ECHO_TIME_MUST_DEFINE are triggered during validation.

"or" arrays are not supported at the lowest level because it wouldn't add any functionality. For example the following is not supported.

{
	"ignore": [
		{
			"or": [
				"ECHO_TIME_GREATER_THAN",
				"ECHO_TIME_NOT_DEFINED"
			]
		}
	]
}

because it would be functionally the same as this:

{
	"ignore": [
		"ECHO_TIME_GREATER_THAN",
		"ECHO_TIME_NOT_DEFINED"
	]
}

For passing a configuration while using the bids-validator on the command line, you can use the following style to for example ignore empty file errors (99) and files that cannot be read (44):

bids-validator --config.ignore=99 --config.ignore=44 path/to/bids/dir

This style of use puts limits on what configuration you can require, so for complex scenarios, we advise users to create a dedicated configuration file with contents as described above.

In the Browser

The BIDS Validator currently works in the browser with browserify or webpack. You can add it to a project by cloning the validator and requiring it with browserify syntax const validate = require('bids-validator'); or an ES2015 webpack import import validate from 'bids-validator'.

On the Server

The BIDS validator works like most npm packages. You can install it by running npm install bids-validator.

Through Command Line

If you install the bids validator globally by using npm install -g bids-validator you will be able to use it as a command line tool. Once installed you should be able to run bids-validator /path/to/your/bids/directory and see any validation issues logged to the terminal. Run bids-validator without a directory path to see available options.

Docker image

Docker Image Version (latest by date)

To use bids validator with docker, you simply need to install docker on your system.

And then from a terminal run:

  • docker run -ti --rm bids/validator --version to print the version of the docker image
  • docker run -ti --rm bids/validator --help to print the help
  • docker run -ti --rm -v /path/to/data:/data:ro bids/validator /data to validate the dataset /path/to/data on your host machine

See here for a brief explanation of the commands:

  • docker run is the command to tell docker to run a certain docker image, usually taking the form docker run <IMAGENAME> <COMMAND>
  • the -ti flag means the inputs are accepted and outputs are printed to the terminal
  • the --rm flag means that the state of the docker container is not saved after it has run
  • the -v flag is adding your local data to the docker container (bind-mounts). Importantly, the input after the -v flag consists of three fields separated colons: :
    • the first field is the path to the directory on the host machine: /path/to/data
    • the second field is the path where the directory is mounted in the container
    • the third field is optional. In our case, we use ro to specify that the mounted data is read only

Python Library

PyPI version

There are is a limited library of helper functions written in Python. The main function determines if a file extension is compliant with the BIDS specification. You can find the available functions in the library, as well as their descriptions, here. To install, run pip install -U bids_validator (requires python and pip).

Example

from bids_validator import BIDSValidator
validator = BIDSValidator()
filepaths = ["/sub-01/anat/sub-01_rec-CSD_T1w.nii.gz", "/sub-01/anat/sub-01_acq-23_rec-CSD_T1w.exe"]
for filepath in filepaths:
    print(validator.is_bids(filepath))  # will print True, and then False

Development

To develop locally, clone the project and run npm install from the project root. This will install external dependencies. If you wish to install bids-validator globally (so that you can run it in other folders), use the following command to install it globally: cd bids-validator && npm install -g (for windows users, if in a different drive add /d, e.g. cd /d F:\bids-validator && npm install -g)

Please see the CONTRIBUTING.md for additional details.

Bundling

bids-validator is bundled with esbuild. While developing, the script bids-validator/bin/bids-validator will automatically bundle the project each time it is run. To test a build without publishing it npm -w bids-validator run build. This will generate a bids-validator/dist directory containing the local build and bids-validator/bin/bids-validator will use this build. To return to automatic bundling on each run, remove the dist directory.

Running Locally in a Browser

A note about OS X, the dependencies for the browser require a npm package called node-gyp which needs xcode to be installed in order to be compiled.

  1. The browser version of bids-validator lives in the repo subdirectory /bids-validator-web. It is a React.js application that uses the next.js framework.
  2. To develop bids-validator and see how it will act in the browser, simply run npm run web-dev in the project root and navigate to localhost:3000.
  3. In development mode, changes to the codebase will trigger rebuilds of the application automatically.
  4. Changes to the /bids-validator in the codebase will also be reflected in the web application.
  5. Tests use the Jest testing library and should be developed in /bids-validator-web/tests. We can always use more tests, so please feel free to contribute a test that reduces the chance of any bugs you fix!
  6. To ensure that the web application compiles successfully in production, run npm run web-export

Testing

If it's your first time running tests, first use the command git submodule update --init --depth 1 to pull the test example data. This repo contains the bids-examples github repository as a submodule.

To start the test suite run npm run test from the project root. npm run test -- --watch is useful to run tests while making changes. A coverage report is available with npm run coverage.

To run the linter which checks code conventions run npm run lint.

Install globally from a development branch

Global installs are not recommended for development because of the possibility of package conflicts with other Node.js projects. If you do need to test with a global install from a development tree, follow these steps to generate the NPM package without publishing it and install the package locally.

  1. npm -w bids-validator run build
  2. npm -w bids-validator pack
  3. npm install -g bids-validator-*.tgz

Publishing

Publishing is done with Lerna. Use the command npx lerna publish and follow instructions to set a new version.

Using lerna publish will create a git commit with updated version information and create a version number tag for it, push the tag to GitHub, then publish to NPM and PyPI. The GitHub release is manual following that.

Acknowledgments

Many contributions to the bids-validator were done by members of the BIDS community. See the list of contributors.

A large part of the development of bids-validator is currently done by Squishymedia, who are in turn financed through different grants offered for the general development of BIDS. See the list below.

Development and contributions were supported through the following federally funded projects/grants: