[Neuroimaging] ANN: Nibabel release 2.2

Christopher Markiewicz effigies at bu.edu
Fri Oct 13 16:30:41 EDT 2017

Hi all,

Nibabel 2.2 has been released, featuring some very long-awaited CIFTI

Other particularly interesting new features are TCK streamlines and
indexed_gzip support, thanks to Marc-Alexandre Côté and Paul McCarthy,

Thanks to all contributors and reviewers, and of course Matthew Brett for
all of his maintenance work.

Please cite using the Zenodo DOI: https://doi.org/10.5281/zenodo.1011207

The full Changelog follows:

New feature release for the 2.2 series.

Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke
Ben Cipollini (BC), Marc-Alexandre Côté (MC), Chris Markiewicz (CM), Stephan
Gerhard (SG) and Eric Larson (EL).

References like "pr/298" refer to github pull request numbers.

New features

* CIFTI support (pr/249) (Satra Ghosh, Michiel Cottaar, BC, CM, Demian
  Wassermann, MB)
* Support for MRtrix TCK streamlines file format (pr/486) (MC, reviewed by
  MB, Arnaud Bore, J-Donald Tournier, Jean-Christophe Houde)
* Added ``get_fdata()`` as default method to retrieve scaled floating point
  data from ``DataobjImage``s (pr/551) (MB, reviewed by CM, Satra Ghosh)


* Support for alternative header field name variants in .PAR files
  (pr/507) (Gregory R. Lee)
* Various enhancements to streamlines API by MC: support for reading TRK
  version 1 (pr/512); concatenation of tractograms using `+`/`+=` operators
  (pr/495); function to concatenate multiple ArraySequence objects (pr/494)
* Support for numpy 1.12 (pr/500, pr/502) (MC, MB)
* Allow dtype specifiers as fileslice input (pr/485) (MB)
* Support "headerless" ArrayProxy specification, enabling memory-efficient
  ArrayProxy reshaping (pr/521) (CM)
* Allow unknown NIfTI intent codes, add FSL codes (pr/528) (Paul McCarthy)
* Improve error handling for ``img.__getitem__`` (pr/533) (Ariel Rokem)
* Delegate reorientation to SpatialImage classes (pr/544) (Mark Hymers, CM,
  reviewed by MB)
* Enable using ``indexed_gzip`` to reduce memory usage when reading from
  gzipped NIfTI and MGH files (pr/552) (Paul McCarthy, reviewed by MB, CM)

Bug fixes

* Miscellaneous MINC reader fixes (pr/493) (Robert D. Vincent, reviewed by
* Fix corner case in ``wrapstruct.get`` (pr/516) (Paul McCarthy, reviewed by
  CM, MB)


* Fix documentation errors (pr/517, pr/536) (Fernando Perez, Venky Reddy)
* Documentation update (pr/514) (Ivan Gonzalez)
* Update testing to use pre-release builds of dependencies (pr/509) (MB)
* Better warnings when nibabel not on path (pr/503) (MB)

API changes and deprecations

* ``header`` argument to ``ArrayProxy.__init__`` is renamed to ``spec``
* Deprecation of ``header`` property of ``ArrayProxy`` object, for removal
* ``wrapstruct.get`` now returns entries evaluating ``False``, instead of
* ``DataobjImage.get_data`` to be deprecated April 2018, scheduled for
  April 2020


Chris Markiewicz
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