Installation

1. 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)

2. 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

3. Then create environment (called MIAW) and install required packages automatically:

  cd Medical_Image_Analysis_Workshop
  conda env create -f environment.yml

4. 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