brainMapper

An open source application that aims to automatize treatments to create a brain function atlas - Industrial Project

About this project

This is an Industrial Project in collaboration with the Central Hospital of Nancy (France). Its aim was to create a tool to automatize the image treatment and clustering application on patients' medical data (NIfTI images, brain region-function associations, etc). This would then allow to create a brain function atlas that can be exported and shared in the neurosciences community.

This tool has thus two components :

• A Python library that ensures all treatments of NIfTI Images and that is the core of this software. It can be used and incorporated into other applications of your making
• A PyQt interface according to the needs of CHRU neurosurgeons

Authors

This project was designed and developped by : Version 1 :

Raphael Agathon
Maxime Cluchague
Graziella Husson (@Graziella-Husson)
Valentina Zelaya (@vz-chameleon)

Version 2 :

Marie Adler
Aurélien Benoît
Thomas Grassellini
Lucie Martin

Getting Started

To install on Linux and Mac (Unix-based) :

To install on Windows :

• Install anaconda for windows: https://www.anaconda.com/download/. Tick the option "Add Anaconda to my PATH variable".
• In a terminal :

conda install python=2.7
activate root
conda install -c anaconda pyqt=4.11.4
conda install numpy
conda install scikit-learn
conda install pyqtgraph
conda install pyopengl
conda install -c conda-forge nibabel

• Download the .zip project on the GitHub repository. Decompress it, and create a .bat file (carefull with the extensions in windows, sometime a .txt will be added and you cannot see it.).
• In the .bat file (This file has to be in the same folder than the decompressed .zip.):

cd brainMapper-master/UI
python UI.py

• Create a .bat shortcut on your Desktop.

License

This project is licensed under the GPL-3 License. All other versions of this software should be released under the same license

Acknowledgments

• Hat tip to Dr Fabien Rech