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