WebMRI: Brain extraction and linear registration in the web browser

Abstract Background and Aim Since the initial release of the World Wide Web, the capabilities of web browsers have grown from presenting formatted documents to running complex programs, such as 3D game engines. The medical imaging community started to adopt technologies that came with the fifth major version of the HyperText Markup Language (HTML5). It led to the creation of various web-based radiological applications such as cornerstone.js or BrainBrowser. BrainBrowser supports both 3D and 2D rendering of neuroimaging data. However, it cannot run important image processing algorithms, such as brain extraction and linear registration, which are essential in most neuroimaging workflows. The most commonly used library that supports these algorithms is the FMRIB Software Library (FSL). We aim to build a web-based cross-platform neuroimaging platform that combines data visualization with image processing. Methods We built our system as an extension of BrainBrowser. We developed WebMRI in JavaScript and designed the user interface using HTML, CSS, and Bootstrap. We used Emscripten to port the brain extraction and linear registration tools of FSL to the web. Results We built WebMRI, a fully web-based extensible neuroimaging platform that combines the visualization capabilities of BrainBrowser with the brain extraction and linear registration tools of FSL by porting them from C++ to WebAssembly. We extended BrainBrowser with a plugin system that makes it easy to bring other processing algorithms into the platform. We released the WebMRI source code on Github: https://github.com/wpmed92/WebMRI . Conclusions We developed and released WebMRI, a web-based cross-platform open-source neuroimaging platform.