README.md

[NiChart] The neuro-imaging brain aging chart

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

cbica.github.io/NiChart/ 🚧

The neuro-imaging brain aging chart [NiChart] is a comprehensive solution to analyze standard structural and functional brain MRI data across studies. [NiChart] 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/NiChart/.

Demonstration of the [NiChart] 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 conda environment

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

Ensure Anaconda is installed. Follow instructions for user's operating system here. After Anaconda has been installed, be sure to exit and reopen any command line windows to use conda command

conda create -n NiChart python=3.8.8  
conda activate NiChart
python -m pip install --upgrade pip

Prepare environment in Linux (CUBIC)

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

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

Install the [NiChart] software

To install the [NiChart], install it in a virtual or conda 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/NiChart.git 
python -m pip install -U -e .
poetry install

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

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

Usage

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

NiChart

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

NiChart --data_file istaging.pkl.gz

Build executable package for Windows 10/11

We use (beeware/briefcase)[https://github.com/beeware/briefcase)] to package the software in Windows 10/11.

briefcase create 
briefcase update
briefcase package

The result is an installer NiChart.msi that will install the app in the user's profile. The installation does not require administrator rights.

Disclaimer

• The software has been designed for research purposes only and has neither been reviewed nor approved for clinical use by the Food and Drug Administration (FDA) or by any other federal/state agency.
• By using NiChart, the user agrees to the following license: https://www.med.upenn.edu/cbica/software-agreement-non-commercial.html

Contact

For more information and support, please post on the Discussions section or contact CBICA Software.