NiBabel

Read / write access to some common neuroimaging file formats

This package provides read +/- write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, CIFTI-2, MINC1, MINC2, AFNI BRIK/HEAD, MGH and ECAT as well as Philips PAR/REC. We can read and write FreeSurfer geometry, annotation and morphometry files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.

The various image format classes give full or selective access to header (meta) information and access to the image data is made available via NumPy arrays.

Website

Current documentation on nibabel can always be found at the NIPY nibabel website.

Mailing Lists

Please send any questions or suggestions to the neuroimaging mailing list.

Code

Install nibabel with:

pip install nibabel

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License

Nibabel is licensed under the terms of the MIT license. Some code included with nibabel is licensed under the BSD license. Please see the COPYING file in the nibabel distribution.

Citing nibabel

Please see the available releases for the release of nibabel that you are using. Recent releases have a Zenodo Digital Object Identifier 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):

  • Yaroslav O. Halchenko

  • Chris Burns

  • Gaël Varoquaux

  • Ian Nimmo-Smith

  • Jarrod Millman

  • Bertrand Thirion

  • Thomas Ballinger

  • Cindee Madison

  • Valentin Haenel

  • Alexandre Gramfort

  • Christian Haselgrove

  • Krish Subramaniam

  • Yannick Schwartz

  • Bago Amirbekian

  • Brendan Moloney

  • Félix C. Morency

  • JB Poline

  • Basile Pinsard

  • Satrajit Ghosh

  • Nolan Nichols

  • Ly Nguyen

  • Philippe Gervais

  • Demian Wassermann

  • Justin Lecher

  • Oliver P. Hinds

  • Nikolaas N. Oosterhof

  • Kevin S. Hahn

  • Michiel Cottaar

  • Erik Kastman

  • Github user freec84

  • Peter Fischer

  • Clemens C. C. Bauer

  • Samuel St-Jean

  • Gregory R. Lee

  • Eric M. Baker

  • Ariel Rokem

  • Eleftherios Garyfallidis

  • Jaakko Leppäkangas

  • Syam Gadde

  • Robert D. Vincent

  • Ivan Gonzalez

  • Demian Wassermann

  • Paul McCarthy

  • Fernando Pérez García

  • Venky Reddy

  • Mark Hymers

  • Jasper J.F. van den Bosch

  • Bennet Fauber

  • Kesshi Jordan

  • Jon Stutters

  • Serge Koudoro

  • Christopher P. Cheng

  • Mathias Goncalves

  • Jakub Kaczmarzyk

  • Dimitri Papadopoulos Orfanos

  • Ross Markello

  • Miguel Estevan Moreno

  • Thomas Roos

  • Igor Solovey

  • Jon Haitz Legarreta Gorroño

  • Katrin Leinweber

  • Soichi Hayashi

  • Samir Reddigari

  • Konstantinos Raktivan

  • Matt Cieslak

  • Egor Panfilov

  • Jath Palasubramaniam

  • Henry Braun

  • Oscar Esteban

  • Cameron Riddell

  • Hao-Ting Wang

  • Dorota Jarecka

  • Chris Gorgolewski

  • Benjamin C Darwin

  • Zvi Baratz

  • Roberto Guidotti

  • Or Duek

  • Anibal Sólon

  • Jonathan Daniel

  • Markéta Calábková

  • Carl Gauthier

  • Julian Klug

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 the appendix 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.