BIDS-Curation-GUI

A Graphical User Interface to help with BIDS Curation

Getting data into the Brain Imaging Data Structure (BIDS) format is non-trivial. Ideally, you set scan acquisition parameters in preparation for BIDS, but mistakes will be made. Non-ideally, you have an old set of scans you want to BIDSify. Wouldn't it be great if you could "see" the entire situation so you can easily locate and understand the problems? Wouldn't you like this picture to come alive to help you curate your data?

We're open to ideas on how to do this and are looking for help from anybody who wants to contribute. The initial plan is to create a basic GUI using React and to base this project on ReproIn, HeuDiConv, and the BIDS-Validator. There will be instructions here on how to download an example data set to get started.

Whether or not you have skills to contribute to the coding, if you are familiar with MRI data acquisition and how it can go wrong we really want your help! We need to know where a graphical user interface can do some good. If you've got graphic design and technical writing skills, please help by working on a project logo, creating artwork for the GUI, and adding documentation.

This project is part of OHBM Brainhack 2020

Build Docker images with Python and JavaScript dev/test requirements installed.

make jsdev-image
make pydev-image

Set the Parcel builder to watch for JavaScript code changes and compile a dev index.js. Run a Flask server that loads the index.js and autoreloads on Python changes.

# In two separate terminals ...
make parcel
make flask

Or, run using ./run.py inputdir outputdir which will do both of those make commands and pass in an input and output directory as environment variables. Use ./stop.py to shut down the docker containers.

Run pytest unit tests. Watch JavaScript files and run Jest tests.

make pytest
make jstest-watch

Build a local production image with Gunicorn and minified JS. Scale three instances of the web app using Docker Compose.

make stack
make unstack

Deploy to a Docker service provider (e.g., ZEIT).

now --docker --public
now ls
now scale <url> 0 3

Flask-react generated from https://github.com/parente/cookiecutter-flask-react template