Installation

Users can install NiChart Project with pip:

pip install NiChart_Project

Alternatively, the package can be installed from source:

git clone https://github.com/CBICA/NiChart_Project
cd NiChart_Project
pip install -r requirements.txt

We release our latest stable version on PyPI; accordingly, we strongly recommend pip installation.

Warning

PyTorch and NumPy have known compatibility issues across different platforms. To avoid potential conflicts, please follow the installation instructions below.

  • After installing all other necessary packages, uninstall any existing Torch installations:

    $ pip uninstall torch

  • Reinstall PyTorch:

    • Linux: PyTorch version 2.3.1

    • Windows: PyTorch version 2.5.1

  • Users can select the correct index URL for their CUDA version based on the PyTorch getting started page

Example on a Linux x86 system:

$ pip install torch==2.3.1 --index-url https://download.pytorch.org/whl/cu121

Managing your environment

We recommend installing NiChart Project within a dedicated environment. Users can create an environment using Mamba (please see Mamba Installation Guide).

Example on a Linux x86 system:

$ wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
  bash Mambaforge-Linux-x86_64.sh
  mamba create -c conda-forge -c bioconda -n NCP_env python=3.12
  mamba activate NCP_env
  git clone https://github.com/CBICA/NiChart_Project.git
  pip install -r requirements.txt