.. -- rest -- .. vim:syntax=rst

.. Use raw location to ensure image shows up on PyPI .. image:: https://raw.githubusercontent.com/nipy/nibabel/master/doc/pics/logo.png :target: https://nipy.org/nibabel :alt: NiBabel logo

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• • Code

    .. image:: https://img.shields.io/pypi/pyversions/nibabel.svg :target: https://pypi.python.org/pypi/nibabel/ :alt: PyPI - Python Version .. image:: https://img.shields.io/badge/code%20style-blue-blue.svg :target: https://blue.readthedocs.io/en/latest/ :alt: code style: blue .. image:: https://img.shields.io/badge/imports-isort-1674b1 :target: https://pycqa.github.io/isort/ :alt: imports: isort .. image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white :target: https://github.com/pre-commit/pre-commit :alt: pre-commit

• • Tests

    .. image:: https://github.com/nipy/NiBabel/actions/workflows/stable.yml/badge.svg :target: https://github.com/nipy/NiBabel/actions/workflows/stable.yml :alt: stable tests .. image:: https://codecov.io/gh/nipy/NiBabel/branch/master/graph/badge.svg :target: https://codecov.io/gh/nipy/NiBabel :alt: codecov badge

• • PyPI

    .. image:: https://img.shields.io/pypi/v/nibabel.svg :target: https://pypi.python.org/pypi/nibabel/ :alt: PyPI version .. image:: https://img.shields.io/pypi/dm/nibabel.svg :target: https://pypistats.org/packages/nibabel :alt: PyPI - Downloads

• • Packages

    .. image:: https://img.shields.io/conda/vn/conda-forge/nibabel :target: https://anaconda.org/conda-forge/nibabel :alt: Conda package .. image:: https://repology.org/badge/version-for-repo/debian_unstable/nibabel.svg?header=Debian%20Unstable :target: https://repology.org/project/nibabel/versions :alt: Debian Unstable package .. image:: https://repology.org/badge/version-for-repo/aur/python:nibabel.svg?header=Arch%20%28%41%55%52%29 :target: https://repology.org/project/python:nibabel/versions :alt: Arch (AUR) .. image:: https://repology.org/badge/version-for-repo/gentoo_ovl_science/nibabel.svg?header=Gentoo%20%28%3A%3Ascience%29 :target: https://repology.org/project/nibabel/versions :alt: Gentoo (::science) .. image:: https://repology.org/badge/version-for-repo/nix_unstable/python:nibabel.svg?header=nixpkgs%20unstable :target: https://repology.org/project/python:nibabel/versions :alt: nixpkgs unstable

• • License & DOI

    .. image:: https://img.shields.io/pypi/l/nibabel.svg :target: https://github.com/nipy/nibabel/blob/master/COPYING :alt: License .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.591597.svg :target: https://doi.org/10.5281/zenodo.591597 :alt: Zenodo DOI

.. Following contents should be copied from LONG_DESCRIPTION in nibabel/info.py

Read and write access to common neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, CIFTI-2, MINC1, MINC2, AFNI BRIK/HEAD, ECAT and Philips PAR/REC. In addition, NiBabel also supports FreeSurfer's MGH, geometry, annotation and morphometry files, and provides some limited support for DICOM.

NiBabel's API gives full or selective access to header information (metadata), and image data is made available via NumPy arrays. For more information, see NiBabel's documentation site and API reference.

.. _API reference: https://nipy.org/nibabel/api.html .. _AFNI BRIK/HEAD: https://afni.nimh.nih.gov/pub/dist/src/README.attributes .. _ANALYZE: http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm .. _CIFTI-2: https://www.nitrc.org/projects/cifti/ .. _DICOM: http://medical.nema.org/ .. _documentation site: http://nipy.org/nibabel .. _ECAT: http://xmedcon.sourceforge.net/Docs/Ecat .. _Freesurfer: https://surfer.nmr.mgh.harvard.edu .. _GIFTI: https://www.nitrc.org/projects/gifti .. _MGH: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat .. _MINC1: https://en.wikibooks.org/wiki/MINC/Reference/MINC1_File_Format_Reference .. _MINC2: https://en.wikibooks.org/wiki/MINC/Reference/MINC2.0_File_Format_Reference .. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/ .. _NIfTI2: http://nifti.nimh.nih.gov/nifti-2/

Installation

To install NiBabel's current release_ with pip, run::

pip install nibabel

To install the latest development version, run::

pip install git+https://github.com/nipy/nibabel

When working on NiBabel itself, it may be useful to install in "editable" mode::

git clone https://github.com/nipy/nibabel.git pip install -e ./nibabel

For more information on previous releases, see the release archive or development changelog.

.. _current release: https://pypi.python.org/pypi/NiBabel .. _release archive: https://github.com/nipy/NiBabel/releases .. _development changelog: https://nipy.org/nibabel/changelog.html

Testing

During development, we recommend using tox_ to run nibabel tests::

git clone https://github.com/nipy/nibabel.git
cd nibabel
tox

To test an installed version of nibabel, install the test dependencies and run pytest_::

pip install nibabel[test]
pytest --pyargs nibabel

For more information, consult the developer guidelines_.

.. _tox: https://tox.wiki .. _pytest: https://docs.pytest.org .. _developer guidelines: https://nipy.org/nibabel/devel/devguide.html

Mailing List

Please send any questions or suggestions to the neuroimaging mailing list <https://mail.python.org/mailman/listinfo/neuroimaging>_.

License

NiBabel is licensed under the terms of the MIT license <https://github.com/nipy/nibabel/blob/master/COPYING#nibabel>_. Some code included with NiBabel is licensed under the BSD license. For more information, please see the COPYING_ file.

.. _BSD license: https://opensource.org/licenses/BSD-3-Clause .. _COPYING: https://github.com/nipy/nibabel/blob/master/COPYING

Citation

NiBabel releases have a Zenodo Digital Object Identifier (DOI) badge at the top of the release notes. Click on the badge for more information.

.. _Digital Object Identifier: https://en.wikipedia.org/wiki/Digital_object_identifier .. _zenodo: https://zenodo.org