Neuroimaging in Python — NiBabel 5.4.0.dev1+g3b1c7b37 documentation (original) (raw)

NiBabel

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.

Installation

To install NiBabel’s current release with pip, run:

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 ordevelopment changelog.

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.

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.

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.

Documentation

See also the Developer documentation page for development discussions, release procedure and more.

Authors and Contributors

Most work on NiBabel so far has been by Matthew Brett, Chris Markiewicz,Michael Hanke, Marc-Alexandre Côté, Ben Cipollini, Paul McCarthy and Chris Cheng. The authors are grateful to the following people who have contributed code and discussion (in rough order of appearance):

License reprise

NiBabel is free-software (beer and speech) and covered by the MIT License. This applies to all source code, documentation, examples and snippets inside the source distribution (including this website). Please see theappendix of the manual for the copyright statement and the full text of the license.

Download and Installation

Please find detailed download and installation instructions in the manual.

Support

If you have problems installing the software or questions about usage, documentation or anything else related to NiBabel, you can post to the NiPy mailing list.

Mailing list:

neuroimaging@python.org [subscription, archive]

We recommend that anyone using NiBabel subscribes to the mailing list. The mailing list is the preferred way to announce changes and additions to the project. You can also search the mailing list archive using the mailing list archive search located in the sidebar of the NiBabel home page.