+
+
+
+
+
+
+## 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](https://git-scm.com/docs/gitignore))
+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.
+
+```Text
+*_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.
+
+```JSON
+{
+ "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**
+
+```JSON
+{
+ "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](https://github.com/bids-standard/bids-validator/blob/master/bids-validator/utils/issues/list.js).
+
+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.
+
+```JSON
+{
+ "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:
+
+```JSON
+{
+ "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.
+
+```JSON
+{
+ "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.
+
+```JSON
+{
+ "ignore": [
+ {
+ "or": [
+ "ECHO_TIME_GREATER_THAN",
+ "ECHO_TIME_NOT_DEFINED"
+ ]
+ }
+ ]
+}
+```
+
+because it would be functionally the same as this:
+
+```JSON
+{
+ "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](https://browserify.org/)
+or [webpack](https://webpack.js.org/). 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
+
+[](https://hub.docker.com/r/bids/validator)
+
+To use bids validator with [docker](https://www.docker.com/), you simply need to
+[install docker](https://docs.docker.com/install/) 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 
