U-fiber tractography

Welcome to the UTracto's Github repository!

Description

This repository contains a package facilitating the tracking of sub-cortical U-Fibers. The main function of this package is the creation of angular maps, enabling a tractography with a position-dependent maximum angle between tractography steps. The function creating these angular maps is wmfod_to_angle in the core.py file.

This angular map is to be used with a forked version of DIPY.

Installing & importing

Online install

The UNRAVEL package is available through pip install under the name utracto. Note that the online version might not always be up to date with the latest changes.

pip install utracto

To upgrade the current version : pip install utracto --upgrade.

To install a specific version of the package use

pip install utracto==0.0.8

All available versions are listed in PyPI. The package names follow the rules of semantic versioning.

Local install

If you want to download the latest version directly from GitHub, you can clone this repository

git clone https://github.com/DelinteNicolas/UTracto.git

For a more frequent use of the library, you may wish to permanently add the package to your current Python environment. Navigate to the folder where this repository was cloned or downloaded (the folder containing the setup.py file) and install the package as follows

cd UTracto
pip install .

If you have an existing install, and want to ensure package and dependencies are updated use --upgrade

pip install --upgrade .

Importing

At the top of your Python scripts, import the library as

import utracto

Checking current version installed

The version of the UNRAVEL package installed can be displayed by typing the following command in your python environment

utracto.__version__

Uninstalling

pip uninstall utracto

Example data and code

An example use of the main methods and outputs of UTracto is written in the example.py file.