0.1.0rc ======= .. warning:: This is the LAST release of Nistats. | All Nistats functionality has been incorporated into Nilearn. | It will be available as part of Nilearn 0.7.0. | All future development will be done in Nilearn. 0.1.0b2 ======= .. warning:: | The phrases `resid` and `w` in method and attribute names | have been changed to `residuals` and `whitened_` respectively. | This will be a breaking change in the stable release of Nistats, | due to be shipped with Nilearn 0.7.0 as `nilearn.stats`. | To minimize compatibility problems, please change the names | according to the info in the "Changes" section. New --- * New example showcasing the use of a GLM to get beta maps for decoding experiments (aka beta-regression). * Addition of all-resolution inference, ie statistically grounded of true positive in given clusters, in :func:`nistats.thresholding.map_threshold` * :func:`nistats.thresholding.map_threshold` can now perform two-sided tests and does so by default. Changes ------- * The following parameters, methods, and attributes have been renamed. Classes affected: `OLSModel`, `RegressionResults`, `LikelihoodModelResults`. * resid -> residuals * df_resid -> df_residuals * norm_resid -> normalized_residuals * wresid -> whitened_residuals * wdesign -> whitened_design * wX -> whitened_X * wY -> whitened_y * `run_img` variable deleted after masking in FirstLevelModel to reduce memory use. * :func:`nistats.reporting.make_glm_report` now uses the computed mask if there is no user-specified one. * Default value of `alpha` in :func:`nistats.reporting.make_glm_report` is `0.001`. Fixes ----- * Explicit method for fixed effects to support image-based summary statistics approach. * FIR delays are now integers. 0.1.0b1 ======= .. warning:: | period_cut (in seconds) has been replaced by high_pass (in Hz) in FirstLevelModel & design matrices. | This is a code-breaking change. Please update your code accordingly. New --- * :func:`nistats.first_level_model.FirstLevelModel` now has the attributes: ``residuals``, ``predicted``, and ``r_square`` which returns a Niimg-like object in the same shape as the input Niimg-like object. Additionally, there is an example showcasing the use of the attributes. * Use :func:`nistats.reporting.make_glm_report` to easily generate HTML reports from fitted first and second level models and contrasts. * New dataset fetcher, :func:`nistats.datasets.fetch_language_localizer_demo_dataset` , BIDS 1.2 compatible. Changes ------- * Nistats now uses BIDS v1.2 & BIDS Derivatives terminology. Fixes ----- * Removed Python 2 deprecation warning for Python 3 installations. * fixed effect contrasts now average effect sizes across runs rather than summing them. * :func:`nistats.first_level_model.first_level_models_from_bids` uses correct BIDS v1.2 conventions. Contributors ------------ The following people contributed to this release (in alphabetical order):: Ana Luisa Pinho Anthony Gifuni Bertrand Thirion Christopher J. Markiewicz Christophe Pallier Gael Varoquaux Jerome Dockes Jerome-Alexis Chevalier Jessica Thompson Kshitij Chawla (kchawla-pi) Takis Panagopoulos Tuan Binh Nguyen 0.0.1b0 ======= Changelog --------- * Updated the minimum versions of the dependencies * Numpy >= 1.11 * SciPy >= 0.17 * Nibabel >= 2.0.2 * Nilearn >= 0.4.0 * Pandas >= 0.18.0 * Sklearn >= 0.18.0 * Added comprehensive tutorial * Second-level model accepts 4D images as input. * Changes in function parameters * third argument of map_threshold is now called ``level``. * Changed the defaut oversampling value for the hemodynamic response to 50 and exposed this parameter. * changed the term ``paradigm`` to ``events`` and made it BIDS-compliant. Set the event file to be tab-separated * ``FirstLevelModel.compute_contrasts`` parameter ``output_type`` can take the value ``'all'``, returning a dictionary of images for each output type * Certain functions and methods have been renamed for clarity * ``nistats.design_matrix`` * ``make_design_matrix() -> make_first_level_design_matrix()`` * ``create_second_level_design() -> make_second_level_design_matrix()`` * ``nistats.utils`` * ``pos_recipr() -> positive_reciprocal()`` * ``multiple_fast_inv() -> multiple_fast_inverse()`` * Python2 Deprecation: Python 2 is now deprecated and will not be supported in a future version. A DeprecationWarning is displayed in Python 2 environments with a suggestion to move to Python 3. Contributors ------------ The following people contributed to this release:: 45 Bertrand Thirion 70 Kshitij Chawla 16 Taylor Salo 6 KamalakerDadi 5 chrplr 5 hcherkaoui 5 rschmaelzle 4 mannalytics 3 Martin Perez-Guevara 2 Christopher J. Markiewicz 1 Loïc Estève 0.0.1a ======= Changelog --------- First alpha release of nistats. Contributors (from ``git shortlog -ns``):: 223 Martin Perez-Guevara 195 bthirion 24 Gael Varoquaux 9 Loïc Estève 3 AnaLu 2 Alexandre Gramfort 1 DOHMATOB Elvis 1 Horea Christian 1 Michael Hanke 1 Salma 1 chrplr