slicerutil 0.2.0

A package created for ease of use working with NumPy in 3D Slicer

slicerutil

A package containing usefull functions for working with common nodes in 3D Slicer as NumPyArrays.

Table of Contents

• Installation
• License
• Requirements
• Setup
• Tutorial
• Example patients
• Acknowledgements

Installation

!!!! Please install this package in a Slicer python environment through 3D Slicer's python terminal !!!!

Install dependencies:

• Python >= 3
• NumPy
• Matplotlib

Install slicerutil

import pip

pip.main(['install', 'slicerutil'])

Import the package

After installing the package use the following to import:

import slicerutil as su

or if you want to use the package in function mode (without oop):

import slicerutil.basic_functions as bf

License

The following repository is under MIT license. For more information, visit LICENSE.

Setup

Downloading the 3D slicer application & supporting software

Please follow the steps provided bellow:

1. Visit slicer to download the application.
2. Visit anaconda to download python3/ jupyter notebook.
3. Visit Visual Studio Code to download the source-code editor (optional).
4. From the Extensions Manager widget, download the SlicerJupyter, MeshToLabelMap, PETDICOMExtension (if working with PET DICOMS), SlicerRT (if working with radiotherapy data).
   • The Slicer application needs to restart to install the extensions.

Set up the SlicerJupyter

1. Using the search widget in Slicer, open the SlicerJupyter extension by searching for JupyterKernel.

   

2. Click the "Start Jupyter Server" button. A JupyterLab notebook will open when the setup is complete.

3. Click the "Jupyter server in external Python environment" and copy the command to clipboard.

4. Open the anaconda prompt (Terminal if on mac) and paste the command.

5. (Optional) open an external environment (Visual Studio Code) and select the Slicer kernel!

Acknowledgements

The slicer scripting tutorial would not be possible without the following open source software:

• Slicer
• Numpy
• Matplotlib