GirderBIDS

A Girder plugin providing support for working with datasets in the Brain Imaging Data Structure (BIDS) format. The project includes:

• A Girder plugin for managing and handling BIDS datasets within Girder.
• A command-line interface (CLI) for validating and importing BIDS datasets into a Girder instance (with or without the plugin).

1. Setup the importer CLI

Ubuntu 22.04:

pip install ".[cli]"

MacOS

curl -fsSL https://deno.land/install.sh | sh
deno compile -ERWN -o bids-validator jsr:@bids/validator
pip install ".[cli]"

Windows

BIDS Validation is not supported but you can still use the plugin and the importer (without validation)

pip install ".[cli]"

2. Install MongoDB

If MongoDB is not already installed on your machine, you can install it following the instructions: https://www.mongodb.com/docs/manual/installation/

Ubuntu

https://www.mongodb.com/docs/manual/tutorial/install-mongodb-enterprise-on-ubuntu/#std-label-install-mdb-enterprise-ubuntu Then:

sudo systemctl start mongod

MacOS

https://www.mongodb.com/docs/manual/tutorial/install-mongodb-enterprise-on-os-x/#std-label-install-enterprise-macos Then:

brew services start mongodb-community

Windows

https://www.mongodb.com/docs/manual/tutorial/install-mongodb-enterprise-on-windows/#std-label-install-enterprise-windows

3. Serve girder

girder serve

You can specify a database other than "girder" by creating a girder.cfg with following content:

[database]
uri = "mongodb://localhost:27017/hint"

And serve girder with GIRDER_CONFIG env variable:

GIRDER_CONFIG=./girder.cfg girder serve

4. Create admin account with "Register" on localhost:8080

5. Login and create API key

6. Create assetstore on localhost:8080

7. Create a Collection copy the ID of the created collection

8. Import BIDS database

bids-importer --bids_dir ... --api_url http://localhost:8080/api/v1  --api_key ... --location_id ...

If you want to ignore the validation step, pass --ignore_validation on the command-line. If you need to upload the dataset directly under a collection or a user, pass --location_type {collection / user / folder} (default is folder). If you want to import the BIDS Dataset using the Girder Plugin, pass --use_plugin on the command-line. If you want to copy BIDS JSON to Girder metadata, pass --extract_metadata on the command-line (works only for dataset_description.json and JSON sidecars).