TIME - Tractography Informed Multi-fascicle microstructure Estimation

Welcome to the TIME's Github repository!

The documentation of the code is available on readthedocs

Description

This repository contains the code used to combine macroscopic tractography information with microscopic multi-fixel model estimates in order to improve the accuracy in the estimation of the microstructural properties of neural fibers in a specified tract.

Installing & importing

Online install

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

pip install TIME-python

To upgrade the current version : pip install TIME-python --upgrade.

To install a specific version of the package use

pip install TIME-python==0.0.4

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/TIME.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 TIME
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 TIME

Checking current version installed

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

TIME.__version__

Uninstalling

pip uninstall TIME-python

Example data and code

An example use of the main methods and outputs of TIME is written in the example.py file. A tractogram of the middle anterior section of the corpus callosum is used as tractography input.