Installation

Requirements

CBPtools requires a Python3 (>=3.5) installation. All of its dependencies will be installed except for FSL’s probtrackx2. This tool is necessary to perform probabilistic tractography on diffusion-weighted imaging data. If you are only interested in using the rsfMRI or connectivity input modalities, probtrackx2 is not necessary.

To see whether probtrackx2 is installed and accessible in your environment, try the following terminal command:

probtrackx2 --help

If it is not available, use these instructions to install FSL.

Installation instructions

It is recommended to use a dedicated virtual environment (see virtualenv documentation):

python3 -m venv ~/.venv/cbptools
source ~/.venv/cbptools/bin/activate

CBPtools can be installed using pip by running the following terminal command:

pip install cbptools

Alternatively, it can be installed directly from GitHub:

pip install git+https://github.com/inm7/cbptools