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@niivue/dcm2niix

@niivue/dcm2niix is a JavaScript + WASM library for converting DICOM files to nifti. This library is intended to be used in the browser, not in a Node.js environment.

All operations are performed using the WASM build of dcm2niix. The processing takes place in a separate worker thread, so it won't block the main thread in your application.

Usage

The @niivue/dcm2niix JavaScript library offers an object oriented API for working with the dcm2niix CLI. Since dcm2niix is a CLI tool, the API implemented in @niivue/dcm2niix is just a wrapper around the CLI options and arguments.

Example

// assuming you have an html input element to get directories.
// <input type="file" id="fileInput" webkitdirectory multiple>
import { Dcm2niix } from '@niivue/dcm2niix';

// use the jpeg import to load jpegls and j2k build of dcm2niix
// import { Dcm2niix } from '@niivue/dcm2niix/jpeg';

const dcm2niix = new Dcm2niix();
// call the init() method to load the wasm before processing any data
await dcm2niix.init();
// fileInput is the id of the input element with options: webkitdirectory and multiple
fileInput.addEventListener('change', async (event) => {
    inputFileList = event.target.files;
});
// inputFileList is the value from the input element with options: webkitdirectory and multiple
const resultFileList = await dcm2niix.input(inputFileList).run()  
console.log(resultFileList);
// Do something with the resultFileList (normal browser File Objects)
// perhaps view them with @niivue/niivue :)

Installation

To install @niivue/dcm2niix in your project, run the following command:

npm install @niivue/dcm2niix

To install a local build of the library

Fist, cd into the js directory of the dcm2niix repository.

# from dcm2niix root directory
cd js

To install a local build of the library, run the following command:

npm run build

Then, install the library using the following command:

npm pack # will create a .tgz file in the root directory

Then, install the @niivue/dcm2niix library in your application locally using the following command:

npm install /path/to/niivue-dcm2niix.tgz

Development

Environment setup

You will need:

  • NodeJS/NPM
  • Emscripten
  • Pixi
  • Make/Cmake

Pixi is used to create the environment for building the WASM port of dcm2niix. To install pixi, follow their instructions.

Note: on macos-arm64, you can get emscripten using homebrew since there is not yet a native arm64 version of emscripten on conda-forge (which is where pixi searches for packages).

Building dcm2niix WASM

pixi run wasm

clean up after build

pixi run clean

If doing things manually

First cd into the js directory of the dcm2niix repository.

# from dcm2niix root directory
cd js

To install the dependencies, run the following command:

npm install

To build the library, run the following command

npm run build

To run the tests, run the following command:

npm run test

Test using a simple demo

To test that the @niivue/dcm2niix library is working correctly, you can run the following command:

npm run demo