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brainprep is a toolbox that provides common Deep Learning brain anatomical, functional and diffusion MR images pre-processing scripts, as well as Quality Control (QC) routines. You can list all available workflows by running the following command in a command prompt:

brainprep --help

The general idea is to provide containers to execute these workflows in order to enforce reproducible research.

This work is made available by a community of people, amoung which the CEA Neurospin BAOBAB laboratory.

• Official source code repo: https://github.com/neurospin-deepinsight/brainprep
• HTML documentation (stable release): https://brainprep.readthedocs.io/en/v0.0.1
• HTML documentation (latest release): https://brainprep.readthedocs.io/en/latest
• Release notes: https://github.com/neurospin-deepinsight/brainprep/blob/master/CHANGELOG.rst

brainprep requires the installation of the following system packages:

• Python [>=3.6]

First make sure you have installed all the dependencies listed above. Then you can install brainprep by running the following command in a command prompt:

pip install -U --user brainprep

More detailed instructions are available at https://brainprep.readthedocs.io/en/latest/generated/installation.html.

The easiest way to get started is to:

• browse available examples: https://brainprep.readthedocs.io/en/latest/auto_gallery/index.html.
• refer to the list of available workflows: https://brainprep.readthedocs.io/en/latest/generated/brainprep.workflow.html.
• refer to the module API documentation: https://brainprep.readthedocs.io/en/latest/generated/brainprep.html.

If you want to contribute to brainprep, be sure to review the contribution guidelines.

There is no paper published yet about brainprep. We suggest that you aknowledge the brainprep team or reference to the code repository: Grigis, A. et al. (2022) BrainPrep source code (Version 0.01) [Source code]. https://github.com/neurospin-deepinsight/brainprep . Thank you.