[NiBAx] The neuro-imaging brain aging chart

| 🚧 This software and documentation is under development! Check out up-to-date documentation at

cbica.github.io/NiBAx/ 🚧

The neuro-imaging brain aging chart [NiBAχ] is a comprehensive solution to analyze standard structural and functional brain MRI data across studies. [NiBAχ] and the associated pre-processing tools implement computational morphometry, functional signal analysis, quality control, statistical harmonization, data standardization, interactive visualization, and extraction of expressive imaging signatures.

This README is intended for contributors and developers. User documentation is available at cbica.github.io/NiBAx/.

Demonstration of the [NiBAχ] graphical user interface.

Setup for development

Install Python version 3.8.8 or newer. The exact procedure depends on the operating system and configuration. Verify the version with

python --version # should be 3.8.8 or newer

Prepare environment in Linux (CUBIC)

Assuming current working directory is NiBAx and containing the source code cloned from https://github.com/CBICA/NiBAx.git.

python -m venv .env
.env/bin/activate
python -m pip install --upgrade pip

Prepare environment for PowerShell (Windows 10 or 11)

Assuming current working directory is NiBAx and containing the source code cloned from https://github.com/CBICA/NiBAx.git.

python -m venv .env
& .env/Scripts/Activate.ps1
python -m pip install --upgrade pip

Install the [NiBAx] software

To install the [NiBAx], install it in a virtual environment. Depending on the desired version, use one of the following commands to install it.

# Editable version for development after cloning https://github.com/CBICA/NiBAx.git 
python -m pip install -U -e . 

# Version from pull request (#57 in this example) for testing proposed changes
python -m pip install -U git+https://github.com/CBICA/NiBAx.git@refs/pull/57/head

# Main version of toolbox
python -m pip install -U git+https://github.com/CBICA/NiBAx.git

Useage

After proper installation, the standalone graphical user interface can be launched in the terminal with:

NiBAx

The data file can be passed as command line argument --data_file as shown below.

NiBAx --data_file istaging.pkl.gz