.. -- 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