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NIPY Changelog

NIPY is not only a module for neuroimaing analysis but an umbrella for other Python neuroimaging-related projects -- see and for more information about their releases.

'Close gh-' statements refer to GitHub issues that are available at:

The full VCS changelog is available here:


Abbreviated authors are:

  • MB - Matthew Brett

  • BT - Bertrand Thirion

  • AR - Alexis Roche

  • GV - Gaël Varoquaux

  • YH - Yarik Halchenko

  • JBP - Jean-Baptiste Poline

  • JT - Jonathan Taylor

  • 0.4.1 (Friday 10 February 2017)

    Bugfix, refactoring and compatibility release.

    • New discrete cosine transform functions for building basis sets;
    • Fixes for compatibility with Python 3.6;
    • Fixes for compatibility with Numpy 1.12 (1.12 no longer allows floating point values for indexing and other places where an integer value is required);
    • Fixes for compatibility with Sympy 1.0;
    • Drop compatibility with Python 2.6, 3.2, 3.3;
    • Add ability to pass plotting arguments to plot_anat function (Matteo Visconti dOC);
    • Some helpers for working with OpenFMRI datasets;
    • Signal upcoming change in return shape from make_recarray when passing in an array for values. Allow user to select upcoming behavior with keyword argument;
    • Bug fix for axis selection when using record arrays in numpies <= 1.7.1;
    • Add flag to allow SpaceTimeRealign to read TR from image headers;
  • 0.4.0 (Saturday 18 October 2015)

    Bugfix, refactoring and compatibility release.

    • Full port to Python 3 using single code-base;
    • Various fixes for modern numpy, scipy, sympy, nibabel compatibility;
    • Refactor space-time realignment (AR);
    • Change in interface for slice-timing options in space-time realign (AR+MB);
    • New nipy_4d_realign script to run space-time realign (Ariel Rokem);
    • Drop requirement for BLAS / LAPACK external library at build-time (AR);
    • Move much code out of nipy.labs into main tree (AR, BT);
    • Deprecate remaining code in nipy.labs (AR, BT);
    • Updates to landmark learning code including API (BT);
    • Various fixes to design matrix machinery (BT, Michael Waskom);
    • Fix to two-sample permutation test suggested by github user jwirsich (BF);
    • Refactoring and fixes to design matrix drift calculations (JBP);
    • Extending API of resampling code to allow more ndimage kwargs (JBP);
    • Start of new example on OpenFMRI ds105 dataset (JT);
    • New block_design function for designs with specified onsets (JT);
    • New show_contrast function for reviewing contrasts (JT);
    • Fix for bug in nipy_diagnose script / screens module giving incorrect PCA output;
    • Added SPM HRF to other HRF options;
    • Redesign concept of an image "space" with new image space modules, functions, classes;
    • Various fixes for correct installation provided or suggested by YH;
    • Some visualization changes by Elvis Dohmatob;
  • 0.3.0 (Saturday 2 February 2013)

    Bugfix, refactoring and compatibility release.

    • Addition of EM algorithm for mixed effects analysis (BT)
    • New high-level GLM class interface (BT)
    • nipy diagnostic scripts save PCA and tsdifana vectors to npz file
    • Python 3 compatibility through 3.3 (MB)
    • Fixes for compatibility with upcoming Numpy 1.7
    • Fixes to background and axis specification in visualization tools (GV, BT)
    • Fixes and tests for installed nipy scripts (MB)
    • Fix to optimization parameters for Realign4D - thanks to bpinsard
    • Fix 0 in affine diagonal for TR=0 in affines by default (MB)
    • Allow saving of nipy images loaded from nifti files that lack explicit affine (MB)
    • Allow slice_order=None to FmriRealign4D when not doing time interpolation (AR); check for valid slice order specification (YH)
    • Refactoring of quantile routine to move code out of C library (AR)
    • Fix bug in resampling of unsigned int images (AR)
    • Custom doctest machinery to work round differences of dtype repr on different platforms, and to skip doctests with optional dependencies (MB)
    • Script to run examples for testing (MB)
    • Fix for accidental integer division of frametimes in design matrix generation (Fabian Pedregosa)
    • Various other fixes and refactorings with thanks from (AR, BT, MB, YH, Yannick Schwartz, Virgile Fritsch)
  • 0.2.0 (Sunday 22 July 2012)

    The first ever official release.

    • > 30 contributors
    • > 6 years in development
    • 192 issues closed on github