NiBabel Development Changelog
NiBabel is the successor to the much-loved PyNifti package. Here we list the
releases for both packages.
‘Close gh-‘ statements refer to GitHub issues that are available at:
The full VCS changelog is available here:
Most work on NiBabel so far has been by Matthew Brett (MB) and Michael Hanke
(MH) and Stephan Gerhard (SG). Recently there have been large contributions from
Krish Subramaniam, Alexandre Gramfort, Cindee Madison, Félix C. Morency,
1.3.0 (Tuesday 11 September 2012)
- New feature and bugfix release
- Add ability to write Freesurfer triangle files (Chris Johnson)
- Relax threshold for detecting rank deficient affines in orientation
detection (JB Poline)
- Fix for DICOM slice normal numerical error (issue #137) (Brendan Moloney)
- Fix for Python 3 error when writing zero bytes for offset padding
1.2.2 (Wednesday 27 June 2012)
- Bugfix release
- Fix longdouble tests for Debian PPC (thanks to Yaroslav Halchecko for
finding and diagnosing these errors)
- Generalize longdouble tests in the hope of making them more robust
- Disable saving of float128 nifti type unless platform has real IEEE
binary128 longdouble type.
1.2.1 (Wednesday 13 June 2012)
Particular thanks to Yaroslav Halchecko for fixes and cleanups in this release
- Bugfix release
- Make compatible with pydicom 0.9.7
- Refactor, rename nifti diagnostic script to nib-nifti-dx
- Fix a bug causing an error when analyzing affines for orientation, when the
affine contained all 0 columns
- Add missing dicomfs script to installation list and rename to
1.2.0 (Sunday 6 May 2012)
- New feature and bugfix release
- Freesurfer format support by Krish Subramaniam and Alexandre Gramfort.
- ECAT read write support by Cindee Madison and Félix C. Morency.
- A DICOM fuse filesystem by Christian Haselgrove.
- Much work on making data scaling on read and write more robust to rounding
error and overflow (MB).
- Import of nipy functions for working with affine transformation matrices.
- Added methods for working with nifti sform and qform fields by Bago
Amirbekian and MB, with useful discussion by Brendan Moloney.
- Fixes to read / write of RGB analyze images by Bago Amirbekian.
- Extensions to concat_images by Yannick Schwartz.
- A new nib-ls script to display information about neuroimaging files, and
various other useful fixes by Yaroslav Halchenko.
1.1.0 (Thursday 28 April 2011)
- New feature release
- Python 3.2 support
- Substantially enhanced gifti reading support (SG)
- Refactoring of trackvis read / write to allow reading and writing of voxel
points and mm points in tracks. Deprecate use of negative voxel sizes;
set voxel_order field in trackvis header. Thanks to Chris Filo
Gorgolewski for pointing out the problem and Ruopeng Wang in the trackvis
forum for clarifying the coordinate system of trackvis files.
- Added routine to give approximate array orientation in form such as ‘RAS’
- Fix numpy dtype hash errors for numpy 1.2.1
- Other bug fixes as for 1.0.2
1.0.2 (Thursday 14 April 2011)
- Bugfix release
- Make inference of data type more robust to changes in numpy dtype hashing
- Fix incorrect thresholds in quaternion calculation (thanks to Yarik H for
pointing this one out)
- Make parrec2nii pass over errors more gracefully
- More explicit checks for missing or None field in trackvis and other
classes - thanks to Marc-Alexandre Cote
- Make logging and error level work as expected - thanks to Yarik H
- Loading an image does not change qform or sform - thanks to Yarik H
- Allow 0 for nifti scaling as for spec - thanks to Yarik H
- nifti1.save now correctly saves single or pair images
1.0.1 (Wednesday 23 Feb 2011)
- Bugfix release
- Fix bugs in tests for data package paths
- Fix leaks of open filehandles when loading images (thanks to Gael
Varoquaux for the report)
- Skip rw tests for SPM images when scipy not installed
- Fix various windows-specific file issues for tests
- Fix incorrect reading of byte-swapped trackvis files
- Workaround for odd numpy dtype comparisons leading to header errors for
some loaded images (thanks to Cindee Madison for the report)
1.0.0 (Thursday, 13, Oct 2010)
- This is the first public release of the NiBabel package.
- NiBabel is a complete rewrite of the PyNifti package in pure python. It was
designed to make the code simpler and easier to work with. Like PyNifti,
NiBabel has fairly comprehensive NIfTI read and write support.
- Extended support for SPM Analyze images, including orientation affines from
matlab .mat files.
- Basic support for simple MINC 1.0 files (MB). Please let us know if you
have MINC files that we don’t support well.
- Support for reading and writing PAR/REC images (MH)
- parrec2nii script to convert PAR/REC images to NIfTI format (MH)
- Very preliminary, limited and highly experimental DICOM reading support (MB,
Ian Nimmo Smith).
- Some functions (nibabel.funcs) for basic image shape changes, including
the ability to transform to the image with data closest to the cononical
image orientation (first axis left-to-right, second back-to-front, third
down-to-up) (MB, Jonathan Taylor)
- Gifti format read and write support (preliminary) (Stephen Gerhard)
- Added utilities to use nipy-style data packages, by rip then edit of nipy
data package code (MB)
- Some improvements to release support (Jarrod Millman, MB, Fernando Perez)
- Huge downward step in the quality and coverage by the docs, caused by MB,
mostly fixed by a lot of good work by MH.
- NiBabel will not work with Python < 2.5, and we haven’t even tested it with
Python 3. We will get to it soon...
Modifications are done by Michael Hanke, if not indicated otherwise. ‘Closes’
statement IDs refer to the Debian bug tracking system and can be queried by
visiting the URL:
- 0.20100706.1 (Tue, 6 Jul 2010)
- Bugfix: NiftiFormat.vx2s() used the qform not the sform. Thanks to Tom
Holroyd for reporting.
- 0.20100412.1 (Mon, 12 Apr 2010)
- Bugfix: Unfortunate interaction between Python garbage collection and C
library caused memory problems. Thanks to Yaroslav Halchenko for the
diagnose and fix.
- 0.20090303.1 (Tue, 3 Mar 2009)
- Bugfix: Updating the NIfTI header from a dictionary was broken.
- Bugfix: Removed left-over print statement in extension code.
- Bugfix: Prevent saving of bogus ‘None.nii’ images when the filename
was previously assign, before calling NiftiImage.save() (Closes: #517920).
- Bugfix: Extension length was to short for all edata whos length matches
n*16-8, for all integer n.
- 0.20090205.1 (Thu, 5 Feb 2009)
- This release is the first in a series that aims stabilize the API and
finally result in PyNIfTI 1.0 with full support of the NIfTI1 standard.
- The whole package was restructured. The included renaming
nifti.nifti(image,format,clibs) to nifti.(image,format,clibs). Redirect
modules make sure that existing user code will not break, but they will
issue a DeprecationWarning and will be removed with the release of PyNIfTI
- Added a special extension that can embed any serializable Python object
into the NIfTI file header. The contents of this extension is
automatically expanded upon request into the .meta attribute of each
NiftiImage. When saving files to disk the content of the dictionary is also
automatically dumped into this extension.
Embedded meta data is not loaded automatically, since this has security
implications, because code from the file header is actually executed.
The documentation explicitely mentions this risk.
- Added NiftiExtensions. This is a container-like
handler to access and manipulate NIfTI1 header extensions.
- Exposed MemMappedNiftiImage in the root module.
- Moved cropImage() into the utils module.
- From now on Sphinx is used to generate the documentation. This includes a
module reference that replaces that old API reference.
- Added methods vx2q() and
vx2s() to convert voxel indices into
coordinates defined by qform or sform respectively.
- Updating the cal_min and cal_max values in the NIfTI header when
saving a file is now conditional, but remains enabled by default.
- Full set of methods to query and modify axis units. This includes
expanding the previous xyzt_units field in the header dictionary into
editable xyz_unit and time_unit fields. The former xyzt_units field
is no longer available. See:
- Full set of methods to query and manuipulate qform and sform codes. See:
- Each image instance is now able to generate a human-readable dump of its
most important header information via __str__().
- NiftiImage objects can now be pickled.
- Switched to NumPy’s distutils for building the package. Cleaned and
simplified the build procedure. Added optimization flags to SWIG call.
- nifti.image.NiftiImage.filename can now also be used to assign a
- Introduced nifti.__version__ as canonical version string.
- Removed updateQFormFromQuarternion() from the list of public methods of
NiftiFormat. This is an internal method that
should not be used in user code. However, a redirect to the new method
will remain in-place until PyNIfTI 1.0.
- Bugfix: getScaledData() returns a
unmodified data array if slope is set to zero (as required by the NIfTI
standard). Thanks to Thomas Ross for reporting.
- Bugfix: Unicode filenames are now handled properly, as long as they do not
contain pure-unicode characters (since the NIfTI library does not support
them). Thanks to Gaël Varoquaux for reporting this issue.
- 0.20081017.1 (Fri, 17 Oct 2008)
- Updated included minimal copy of the nifticlibs to version 1.1.0.
- Few changes to the Makefiles to enhance Posix compatibility. Thanks to
- When building on non-Debian systems, only add include and library paths
pointing to the local nifticlibs copy, when it is actually built.
On Debian system the local copy is still not used at all, as a proper
nifticlibs package is guaranteed to be available.
- Added minimal setup_egg.py for setuptools users. Thanks to Gaël Varoquaux.
- PyNIfTI now does a proper wrapping of the image data with NumPy arrays,
which no longer leads to accidental memory leaks, when accessing array
data that has not been copied before (e.g. via the data property of
NiftiImage). Thanks to Gaël Varoquaux for mentioning this possibility.
- 0.20080710.1 (Thu, 7 Jul 2008)
- Bugfix: Pointer bug introduced by switch to new NumPy API in 0.20080624
Thanks to Christopher Burns for fixing it.
- Bugfix: Honored DeprecationWarning: sync() -> flush() for memory mapped
arrays. Again thanks to Christopher Burns.
- More unit tests and other improvements (e.g. fixed circular imports) done
by Christopher Burns.
- 0.20080630.1 (Tue, 30 Jun 2008)
- Bugfix: NiftiImage caused a memory leak by not calling the NiftiFormat
- Bugfix: Merged bashism-removal patch from Debian packaging.
- 0.20080624.1 (Tue, 24 Jun 2008)
- Converted all documentation (including docstrings) into the restructured
- Improved Makefile.
- Included configuration and Makefile support for profiling, API doc
generation (via epydoc) and code quality checks (with PyLint).
- Consistently import NumPy as N.
- Bugfix: Proper handling of [qs]form codes, which previously have not been
handled at all. Thanks to Christopher Burns for pointing it out.
- Bugfix: Make NiftiFormat work without setFilename(). Thanks to Benjamin
Thyreau for reporting.
- Bugfix: setPixDims() stored meaningless values.
- Use new NumPy API and replace deprecated function calls
- Initial support for memory mapped access to uncompressed NIfTI files
- Add a proper Makefile and setup.cfg for compiling PyNIfTI under Windows
- Include a minimal copy of the most recent nifticlibs (just libniftiio and
znzlib; version 1.0), to lower the threshold to build PyNIfTI on systems
that do not provide a developer package for those libraries.
- 0.20070930.1 (Sun, 30 Sep 2007)
- 0.20070917.1 (Mon, 17 Sep 2007)
- Bugfix: Can now update NIfTI header data when no filename is set
- Unloading of image data without a filename set is no checked and prevented
as it would damage data integrity and the image data could not be
- Added ‘pixdim’ property (Yaroslav Halchenko).
- 0.20070905.1 (Wed, 5 Sep 2007)
- Fixed a bug in the qform/quaternion handling that caused changes to the
qform to vanish when saving to file (Yaroslav Halchenko).
- Added more unit tests.
- ‘dim’ vector in the NIfTI header is now guaranteed to only contain
non-zero elements. This caused problems with some applications.
- 0.20070803.1 (Fri, 3 Aug 2007)
- Does not depend on SciPy anymore.
- Initial steps towards a unittest suite.
- pynifti_pst can now print the peristimulus signal matrix for a single
voxel (onsets x time) for easier processing of this information in
- utils.getPeristimulusTimeseries() can now be used to compute mean and
variance of the signal (among others).
- pynifti_pst is able to compute more than just the mean peristimulus
timeseries (e.g. variance and standard deviation).
- Set default image description when saving a file if none is present.
- Improved documentation.
- 0.20070425.1 (Wed, 25 Apr 2007)
- Improved documentation. Added note about the special usage of the header
property. Also added notes about the relevant properties in the docstring
of the corresponding accessor methods.
- Added property and accessor methods to access/modify the repetition time
of timeseries (dt).
- Added functions to manipulate the pixdim values.
- Added utils.py with some utility functions.
- Added functions/property to determine the bounding box of an image.
- Fixed a bug that caused a corrupted sform matrix when converting a NumPy
array and a header dictionary into a NIfTI image.
- Added script to compute peristimulus timeseries (pynifti_pst).
- Package now depends on python-scipy.
- 0.20070315.1 (Thu, 15 Mar 2007)
- Removed functionality for “NiftiImage.save() raises an IOError
exception when writing the image file fails.” (Yaroslav Halchenko)
- Added ability to force a filetype when setting the filename or saving
- Reverse the order of the ‘header’ and ‘load’ argument in the NiftiImage
constructor. ‘header’ is now first as it seems to be used more often.
- Improved the source code documentation.
- Added getScaledData() method to NiftiImage that returns a copy of the data
array that is scaled with the slope and intercept stored in the NIfTI
- 0.20070301.2 (Thu, 1 Mar 2007)
- Fixed wrong link to the source tarball in README.html.
- 0.20070301.1 (Thu, 1 Mar 2007)
- Initial upload to the Debian archive. (Closes: #413049)
- NiftiImage.save() raises an IOError exception when writing the image file
- Added extent, volextent, and timepoints properties to NiftiImage
class (Yaroslav Halchenko).
- 0.20070220.1 (Tue, 20 Feb 2007)
- NiftiFile class is renamed to NiftiImage.
- SWIG-wrapped libniftiio functions are no available in the nifticlib
- Fixed broken NiftiImage from Numpy array constructor.
- Added initial documentation in README.html.
- Fulfilled a number of Yarik’s wishes ;)
- 0.20070214.1 (Wed, 14 Feb 2007)
- Does not depend on libfslio anymore.
- Up to seven-dimensional dataset are supported (as much as NIfTI can do).
- The complete NIfTI header dataset is modifiable.
- Most image properties are accessable via class attributes and accessor
- Improved documentation (but still a long way to go).
- 0.20061114 (Tue, 14 Nov 2006)