GirderBIDS

Girder plugin to import a BIDS database

1. Setup

Ubuntu 22.04:

pip install girder girder-client fire bids-validator-deno

MacOS

curl -fsSL https://deno.land/install.sh | sh
deno compile -ERWN -o bids-validator jsr:@bids/validator
pip install girder girder-client fire

Windows

Not currently supported.

2. Build girder front

Ubuntu 22.04

girder build

MacOS

Install npm using Homebrew :

brew install node

Add the following environment variable:

export NODE_OPTIONS=--openssl-legacy-provider

girder build

3. Install mongodb

Ubuntu 22.04

To set up MongoDB 4.4 on Ubuntu 22.04 execute the following commands :

curl -fsSL https://pgp.mongodb.com/server-4.4.asc | sudo gpg -o /usr/share/keyrings/mongodb-server-4.4.gpg --dearmor
echo "deb [ arch=amd64,arm64 signed-by=/usr/share/keyrings/mongodb-server-4.4.gpg ] https://repo.mongodb.org/apt/ubuntu focal/mongodb-org/4.4 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-4.4.list
apt-get update
wget http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1f-1ubuntu2_amd64.deb
sudo dpkg -i libssl1.1_1.1.1f-1ubuntu2_amd64.deb
apt-get install -y mongodb-org mongo-tools
sudo systemctl daemon-reload
systemctl start mongod
systemctl enable mongod
chown mongodb:mongodb /var/log/mongodb/mongod.log
chown -R mongodb:mongodb /var/lib/mongodb/*

MacOS

Add MongoDB 4.4:

brew tap mongodb/brew
brew install mongodb-community@4.4
brew services start mongodb-community@4.4

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 and a Folder in the collection, copy the ID of the created Folder

8. Import BIDS database

python tools/bids-importer.py  --bids_dir ... --girder_api_url http://localhost:8080/api/v1  --girder_api_key ... --girder_folder_id ...

If you want to ignore the validation step, pass --ignore_validation on the command-line.