Usage

Development

Release

brainprep

What is brainprep?

brainprep is a comprehensive toolbox designed to streamline the preprocessing of brain MRI data for deep learning applications. It offers a suite of standardized scripts tailored for anatomical, functional, and diffusion magnetic resonance imaging (MRI), ensuring consistent and high-quality data preparation across studies. In addition to preprocessing pipelines, brainprep includes robust quality control (QC) routines to help researchers assess data integrity and detect potential artifacts or anomalies.

To explore the full range of available workflows, simply run the following command in your terminal:

brainprep --help

Each workflow is encapsulated within a containerized environment, promoting reproducibility and simplifying deployment across different systems. By leveraging container technology, brainprep minimizes dependency issues and ensures that preprocessing steps can be executed reliably, regardless of the underlying hardware or operating system.

Whether you're working on large-scale neuroimaging datasets or developing novel deep learning models for brain analysis, brainprep provides a modular, scalable, and reproducible foundation to accelerate your research.

Important Links

• Official source code repo: https://github.com/brainprepdesk/brainprep
• HTML documentation (stable release): https://brainprepdesk.github.io/brainprep/stable
• HTML documentation (dev): https://brainprepdesk.github.io/brainprep/dev

Install

Latest release

1. Setup a virtual environment

We recommend that you install brainprep in a virtual Python environment, either managed with the standard library venv or with conda. Either way, create and activate a new python environment.

With venv:

python3 -m venv /<path_to_new_env>
source /<path_to_new_env>/bin/activate

Windows users should change the last line to \<path_to_new_env>\Scripts\activate.bat in order to activate their virtual environment.

With conda:

conda create -n brainprep python=3.12
conda activate brainprep

2. Install brainprep with pip

Execute the following command in the command prompt / terminal in the proper python environment:

python3 -m pip install -U brainprep

Check installation

Try importing brainprep in a Python / iPython session:

import brainprep

If no error is raised, you have installed brainprep correctly.

Dependencies

The required dependencies to use the software are listed in the file pyproject.toml.

Citation

There is no paper published yet about brainprep. We suggest that you aknowledge the brainprep team or reference to the code repository. Thank you.

@misc{brainprep,
    title = {{BrainPrep source code (Version 1.0.0)}},
    author = {Grigis, Antoine and Victor, Julie and Dorval, Loic and Duchesnay, Edouard},
    url = {https://github.com/brainprepdesk/brainprep},
}