.. -*- rest -*-
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.. 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
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* - Tests
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.. image:: https://codecov.io/gh/nipy/NiBabel/branch/master/graph/badge.svg
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:alt: codecov badge
* - PyPI
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:alt: PyPI version
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* - Packages
-
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:target: https://anaconda.org/conda-forge/nibabel
:alt: Conda package
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* - License & DOI
-
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:alt: License
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.. 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
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Following contents should be copied from LONG_DESCRIPTION in nibabel/info.py\n\n\nRead and write access to common neuroimaging file formats, including:\nANALYZE_ (plain, SPM99, SPM2 and later), GIFTI_, NIfTI1_, NIfTI2_, `CIFTI-2`_,\nMINC1_, MINC2_, `AFNI BRIK/HEAD`_, ECAT_ and Philips PAR/REC.\nIn addition, NiBabel also supports FreeSurfer_'s MGH_, geometry, annotation and\nmorphometry files, and provides some limited support for DICOM_.\n\nNiBabel's API gives full or selective access to header information (metadata),\nand image data is made available via NumPy arrays. For more information, see\nNiBabel's `documentation site`_ and `API reference`_.\n\n.. _API reference: https://nipy.org/nibabel/api.html\n.. _AFNI BRIK/HEAD: https://afni.nimh.nih.gov/pub/dist/src/README.attributes\n.. _ANALYZE: http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm\n.. _CIFTI-2: https://www.nitrc.org/projects/cifti/\n.. _DICOM: http://medical.nema.org/\n.. _documentation site: http://nipy.org/nibabel\n.. _ECAT: http://xmedcon.sourceforge.net/Docs/Ecat\n.. _Freesurfer: https://surfer.nmr.mgh.harvard.edu\n.. _GIFTI: https://www.nitrc.org/projects/gifti\n.. _MGH: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat\n.. _MINC1:\n https://en.wikibooks.org/wiki/MINC/Reference/MINC1_File_Format_Reference\n.. _MINC2:\n https://en.wikibooks.org/wiki/MINC/Reference/MINC2.0_File_Format_Reference\n.. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/\n.. _NIfTI2: http://nifti.nimh.nih.gov/nifti-2/\n\nInstallation\n============\n\nTo install NiBabel's `current release`_ with ``pip``, run::\n\n pip install nibabel\n\nTo install the latest development version, run::\n\n pip install git+https://github.com/nipy/nibabel\n\nWhen working on NiBabel itself, it may be useful to install in \"editable\" mode::\n\n git clone https://github.com/nipy/nibabel.git\n pip install -e ./nibabel\n\nFor more information on previous releases, see the `release archive`_ or\n`development changelog`_.\n\n.. _current release: https://pypi.python.org/pypi/NiBabel\n.. _release archive: https://github.com/nipy/NiBabel/releases\n.. _development changelog: https://nipy.org/nibabel/changelog.html\n\nTesting\n=======\n\nDuring development, we recommend using tox_ to run nibabel tests::\n\n git clone https://github.com/nipy/nibabel.git\n cd nibabel\n tox\n\nTo test an installed version of nibabel, install the test dependencies\nand run pytest_::\n\n pip install nibabel[test]\n pytest --pyargs nibabel\n\nFor more information, consult the `developer guidelines`_.\n\n.. _tox: https://tox.wiki\n.. _pytest: https://docs.pytest.org\n.. _developer guidelines: https://nipy.org/nibabel/devel/devguide.html\n\nMailing List\n============\n\nPlease send any questions or suggestions to the `neuroimaging mailing list\n<https://mail.python.org/mailman/listinfo/neuroimaging>`_.\n\nLicense\n=======\n\nNiBabel is licensed under the terms of the `MIT license\n<https://github.com/nipy/nibabel/blob/master/COPYING#nibabel>`__.\nSome code included with NiBabel is licensed under the `BSD license`_.\nFor more information, please see the COPYING_ file.\n\n.. _BSD license: https://opensource.org/licenses/BSD-3-Clause\n.. _COPYING: https://github.com/nipy/nibabel/blob/master/COPYING\n\nCitation\n========\n\nNiBabel releases have a Zenodo_ `Digital Object Identifier`_ (DOI) badge at\nthe top of the release notes. 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