[niCHART] The neuro-imaging brain aging chart

| :construction: This software and documentation is under development! Check out up-to-date documentation at cbica.github.io/niCHART/ :construction: | |-----------------------------------------|

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/.

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

shell 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

shell 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.

shell 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.

shell 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.

```shell

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:

shell niCHART

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

shell 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.

shell 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.