- To set the virtual environment to run this tutorial we will use conda. If you do not have you can install one of these two options:
- Anaconda (management system with some packages already built in)
- Miniconda (management system without packages)
- Clone this repository or download the .zip file to your documents folder (to clone the repository you need to have git install):
- clone repository in Windows using the following commands on your Anaconda Powershell Prompt (replace <current_user> by your user name):
cd C:\Users\<current_user>\Documents\
git clone https://github.com/JoaoSantinha/Medical_Image_Analysis_Workshop.git
- clone repository in Mac/Linux using the following commands on your terminal:
cd ~/Documents
git clone https://github.com/JoaoSantinha/Medical_Image_Analysis_Workshop.git
- Then create environment (called MIAW) and install required packages automatically:
cd Medical_Image_Analysis_Workshop
conda env create -f environment.yml
- Activate environment and install required Jupyter Lab extensions:
conda activate MIAW
conda install -c conda-forge nodejs
npm install -g configurable-http-proxy
jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-matplotlib jupyterlab-datawidgets itkwidgets
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