JoaoSantinha / Medical_Image_Analysis_Workshop

Workshop on Medical Image Analysis using pydicom, SimpleITK, ITK, itkwidgets, numpy, seaborn, and matplotlib

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