:construction: This software and documentation is under development! Check out up-to-date documentation at cbica.github.io/niCHART/ :construction: |
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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/.
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
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
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
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
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
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
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.
For more information and support, please post on the Discussions section or contact CBICA Software.