neurospin/brainprep-fmriprep repository overview

⁠brainprep: tools for brain MRI Deep Learning pre-processing

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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.

⁠Important links

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

⁠Dependencies

brainprep requires the installation of the following system packages:

• Python [>=3.6]

⁠Install

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.

⁠Where to start

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.

⁠Contributing

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

⁠Citation

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.