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nilearn

0.10.3

HIGHLIGHTS

Warning

Minimum supported versions of packages have been bumped up:
- Numpy -- v1.19.0
- SciPy -- v1.8.0
- Scikit-learn -- v1.0.0
- Nibabel -- v4.0.0
- Pandas -- v1.1.5
- Joblib -- v1.0.0
  • API Allow passing arguments to ~nilearn.glm.first_level.first_level_from_bids to build first level models that include specific set of confounds by relying on the strategies from ~nilearn.interfaces.fmriprep.load_confounds (4103 by Rémi Gau).
  • API Support passing t and F contrasts to ~nilearn.glm.compute_contrast that that have fewer columns than the number of estimated parameters. Remaining columns are padded with zero (4067 by Rémi Gau).
  • API ~maskers.NiftiSpheresMasker now has generate_report method (3102 by Yasmin Mzayek and Nicolas Gensollen).
  • Code Update the CompCor strategy in ~interfaces.fmriprep.load_confounds and ~interfaces.fmriprep.load_confounds_strategy to support fmriprep 21.x series and above. (3285 by Hao-Ting Wang).
  • Doc Combine GLM examples plot_fixed_effect and plot_fiac_analysis into a a single example plot_two_runs_model (3191 by Taylor Salo and Rémi Gau).
  • Plotting Allow setting vmin in ~nilearn.plotting.plot_glass_brain and ~nilearn.plotting.plot_stat_map (3993 by Michelle Wang).
  • Plotting When plotting thresholded statistical maps with a colorbar, the threshold value(s) will now be displayed as tick labels on the colorbar (#2833 by Nicolas Gensollen).

NEW

  • Plotting The temp_file_lifetime parameter of interactive plots' open_in_browser method is deprecated and has no effect (4180 by Jerome Dockes)..

Fixes

  • API ~maskers.MultiNiftiMasker can now call ~maskers.NiftiMasker.generate_report which will generate a report for the first subject in the list of subjects (4001 by Yasmin Mzayek).
  • Code Make sure that all atlases and datasets fetchers return a description (4215 Rémi Gau).
  • Code Update the CompCor strategy in ~interfaces.fmriprep.load_confounds and ~interfaces.fmriprep.load_confounds_strategy to support fmriprep 21.x series and above. (3285 by Hao-Ting Wang).
  • Code Fix ~nilearn.glm.regression.SimpleRegressionResults to accommodate for the lack of a model attribute (4071 Rémi Gau)
  • Code ~image.clean_img can now use kwargs clean__sample_mask argument to correctly reshape the nifti image to the dimensions of the mask in the output (4051 by Mia Zwally).
  • Code Fix plotting of an image with color bar when maximum value is exactly zero (4204 by Rémi Gau).
  • Code Fix PSC normalisation method applied by standardize_signal in ~nilearn.signal (4116 by Hao-Ting Wang and Yasmin Mzayek).
  • Code Fixed inheritance of decoder classes to keep compatibility with scikit-learn>v1.3 (4188 by Yasmin Mzayek).
  • Deprecation Make sure that all the fetchers for atlas and func from nilearn.datasets return a sklearn.utils.Bunch. Add new behavior to ~datasets.fetch_language_localizer_demo_dataset to return output as Bunch. This behavior will become the default in version 0.13.0 (4233 by Rémi Gau).

Enhancements

  • API ~maskers.NiftiSpheresMasker now has generate_report method (3102 by Yasmin Mzayek and Nicolas Gensollen).
  • API Allow passing Pandas Series of image filenames to ~nilearn.glm.second_level.SecondLevelModel (4070 by Rémi Gau).
  • API Allow passing arguments to ~nilearn.glm.first_level.first_level_from_bids to build first level models that include specific set of confounds by relying on the strategies from ~nilearn.interfaces.fmriprep.load_confounds (4103 by Rémi Gau).
  • API Support passing t and F contrasts to ~nilearn.glm.compute_contrast that that have fewer columns than the number of estimated parameters. Remaining columns are padded with zero (4067 by Rémi Gau).
  • Code Multi-subject maskers' generate_report method no longer fails with 5D data but instead shows report of first subject. User can index input list to show report for different subjects (3935 by Yasmin Mzayek).
  • Code Allow global_signal parameter in ~interfaces.fmriprep.load_confounds_strategy in denoise_strategy='compcor' (4225 by Hao-Ting Wang).
  • Code Add two_sided option for ~nilearn.image.binarize_img (4121 by Steven Meisler).
  • Code ~maskers.NiftiLabelsMasker.generate_report now uses appropriate cut coordinates when functional image is provided (4099 by Yasmin Mzayek and Nicolas Gensollen).
  • Doc Mention the classification type (all-vs-one) in sphx_glr_auto_examples_02_decoding_plot_haxby_glm_decoding.py (4122 by Tamer Gezici).
  • Doc Add backslash to homogenize ~nilearn.regions.Parcellations documentation (4042 by Nikhil Krish).
  • Doc Specify full form of LSS in sphx_glr_auto_examples_07_advanced_plot_beta_series.py (4141 by Tamer Gezici).
  • Doc Don't fetch tmaps in examples if tmaps aren't used in the example. (4136 by Christina Roßmanith).
  • Doc Describe the return value in ~nilearn.datasets.fetch_abide_pcp documentation (4159 by Suramya Pokharel).
  • Plotting Allow setting vmin in ~nilearn.plotting.plot_glass_brain and ~nilearn.plotting.plot_stat_map (3993 by Michelle Wang).
  • Plotting When plotting thresholded statistical maps with a colorbar, the threshold value(s) will now be displayed as tick labels on the colorbar (#2833 by Nicolas Gensollen).

Changes

  • API Expose scipy CubicSpline extrapolate parameter in ~signal.clean to control the interpolation of censored volumes in both ends of the BOLD signal data (4028 by Jordi Huguet).
  • Code Make nilearn.reporting._get_clusters_table module public and move copy_img out of nilearn._utils.niimg (4166 by Rémi Gau).
  • Code Private utility context manager write_tmp_imgs is refactored into function write_imgs_to_path (4094 by Yasmin Mzayek).
  • Code Move user facing function concat_niimgs out of private module nilearn._utils.niimg_conversions (4167 by Rémi Gau).
  • Code Remove leading underscore from non private functions to align with PEP8 (4086 by Rémi Gau).
  • Code Make decoding/proximal_operator explicitly private to align with PEP8 (4153 by Rémi Gau).
  • Code Make private functions public when used outside of their module nilearn.interface to align with PEP8 (4168 by Rémi Gau).
  • Deprecation ~regions.img_to_signals_labels will also return masked_atlas in release 0.15. Meanwhile, use return_masked_atlas parameter to enable/disable this behavior. (3761 by Mohammad Torabi).
  • Deprecation Rename the parameter contrast_type in ~glm.compute_contrast and attribute contrast_type in ~glm.Contrast to stat_type (4191 by Rémi Gau).
  • Deprecation ~plotting.plot_surf_roi will raise a warning if roi_map contains negative or non-integer values; in version 0.13 this will be a ValueError (4131 by Michelle Wang).
  • Deprecation nilearn.datasets.fetch_bids_langloc_dataset will be deprecated in release 0.13 as it returns data simuilar to ~.datasets.fetch_language_localizer_demo_dataset (4219 by Rémi Gau).
  • Deprecation the default parameter of fd_threshold and std_dvars_threshold in ~interfaces.fmriprep.load_confounds with be updated to match fmriprep default in version 0.13 (4225 by Hao-Ting Wang).
  • Doc Combine GLM examples plot_fixed_effect and plot_fiac_analysis into a a single example plot_two_runs_model (3191 by Taylor Salo and Rémi Gau).
  • Maint Switch to using tox to manage environments during development and testing. All plotting python dependencies (matplotlib AND plotly) are now installed when running pip install nilearn[plotting] (4029 by Rémi Gau).