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https://github.com/nipy/nibabel

Python package to access a cacophony of neuro-imaging file formats
https://github.com/nipy/nibabel

afni-brik-head brain-imaging cifti-2 data-formats dicom ecat gifti minc neuroimaging nifti python streamlines tck trk

Last synced: 5 days ago
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Python package to access a cacophony of neuro-imaging file formats

Host: GitHub
URL: https://github.com/nipy/nibabel
Owner: nipy
License: other
Created: 2010-07-22T16:28:30.000Z (over 14 years ago)
Default Branch: master
Last Pushed: 2024-10-15T18:39:15.000Z (21 days ago)
Last Synced: 2024-10-17T02:47:55.543Z (19 days ago)
Topics: afni-brik-head, brain-imaging, cifti-2, data-formats, dicom, ecat, gifti, minc, neuroimaging, nifti, python, streamlines, tck, trk
Language: Python
Homepage: http://nipy.org/nibabel/
Size: 18.3 MB
Stars: 650
Watchers: 37
Forks: 258
Open Issues: 130
Metadata Files:
- Readme: README.rst
- Changelog: Changelog
- Contributing: .github/CONTRIBUTING.md
- License: COPYING
- Code of conduct: .github/CODE_OF_CONDUCT.md

Awesome Lists containing this project

awesome-neuroscience - NiBabel - Provides read and write access to some common medical and neuroimaging file formats. (Programming / Python)
awesome-neuroscience - NiBabel - Provides read and write access to some common medical and neuroimaging file formats. (Programming / Python)
awesome-python-machine-learning-resources - GitHub - 26% open · ⏱️ 20.08.2022): (医疗领域)

README

.. -*- 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

.. list-table::
:widths: 20 80
:header-rows: 0

* - 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
`_.

License
=======

NiBabel is licensed under the terms of the `MIT license
`__.
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