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A wrapper for generating Docker and Singularity commands for simpler NiBabies usage

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Project description

The NiBabies Docker/Singularity wrapper

NiBabies is a functional magnetic resonance image pre-processing pipeline optimized for infant and neonate MRI. It is designed to provide an easily accessible, state-of-the-art interface that is robust to differences in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

This is a Python wrapper to run NiBabies. It generates the appropriate Docker or Singularity commands, providing an intuitive interface to running the fMRIPrep workflow in whichever environment. Docker or Singularity must be installed, and in the case of Docker, running. Installations can be check by running

docker info  # Docker
singularity version  # Singularity

Please report any feedback to our GitHub repository and do not forget to credit all the authors of software that NiBabies uses.

Usage

Example Docker usage

nibabies-wrapper docker <data-path> <output-path> participant <nibabies-arguments>

Example Singularity usage

nibabies-wrapper singularity <data-path> <output-path> participant -i <img-path> <nibabies-arguments>

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