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 nistats.thresholding.map_threshold

• 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.

• nistats.reporting.make_glm_report now uses the computed mask if there is no user-specified one.

• Default value of alpha in 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period_cut (in seconds) has been replaced by high_pass (in Hz) in FirstLevelModel & design matrices.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

• 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 nistats.reporting.make_glm_report to easily generate HTML reports from fitted first and second level models and contrasts.

• New dataset fetcher, 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.

• 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