Setup: How to setup and run the tutorial

Tutorial: How to create a BIDS dataset

Download notebooks

Download notebooks from the right sidebar. Select Colab if you are using Google Colab.

Computational environments

JupyterHub at UHH

1. Open https://code.min.uni-hamburg.de/

2. Select File > New Launcher

3. At the bottom, select Terminal

4. In the Terminal, enter:

   git clone https://github.com/lnnrtwttkhn/rdm-bids
   cd rdm-bids
   make install

5. From the sidebar on the left, you can now open the exercise notebooks in the rdm-bids folder:

   • exercise1.ipynb
   • exercise2.ipynb

6. Paste the installation command into the first cell of the notebook:

   source .venv/bin/activate

Google Colab

1. Open https://colab.research.google.com/
2. Sign in with a Google account
3. Select File > Open notebook
4. Select Upload and open or drag the notebook file
5. Paste the installation command into the first cell of the notebook:

!apt-get install tree
pip install bash-kernel>=0.10.0 bids-validator-deno>=2.3.1 dcm2niix>=1.0.20250506 heudiconv>=1.3.4 ipykernel>=7.1.0 jupyter>=1.1.1 nbformat>=5.10.4 pandas>=3.0.0

Terminal

1. Open a Terminal and copy-paste all commands in the exercise