Skip to main content

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>

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

nibabies_wrapper-23.0.0.tar.gz (10.7 kB view details)

Uploaded Source

Built Distribution

nibabies_wrapper-23.0.0-py2.py3-none-any.whl (12.0 kB view details)

Uploaded Python 2 Python 3

File details

Details for the file nibabies_wrapper-23.0.0.tar.gz.

File metadata

  • Download URL: nibabies_wrapper-23.0.0.tar.gz
  • Upload date:
  • Size: 10.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.10.9

File hashes

Hashes for nibabies_wrapper-23.0.0.tar.gz
Algorithm Hash digest
SHA256 706e8b09c39c24a20996bfe2cbe733d4567184d6b377e29d45f2248486dfea80
MD5 2999da9b7e4b900240d8720889fb3392
BLAKE2b-256 2bf89b1aa965bb797f49d0639e08b3d487dc27531650b84bb21bb66f9a8ca1fc

See more details on using hashes here.

File details

Details for the file nibabies_wrapper-23.0.0-py2.py3-none-any.whl.

File metadata

File hashes

Hashes for nibabies_wrapper-23.0.0-py2.py3-none-any.whl
Algorithm Hash digest
SHA256 5e70abd2e142076db67c30478df20aacdf9fc7fdfbb505d6a5e55b33d1f5c4cf
MD5 ea25c65adf603d8e785caf9fa4a0a343
BLAKE2b-256 caf72d5f5452449bd78e0916b47549ad86340cded81076f0fdaf0d16750969c8

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page