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0.10.2.rst

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nilearn

0.10.2

Released September 2023

HIGHLIGHTS

  • Plotting Volume plotting functions like ~plotting.plot_img now have an optional radiological parameter, defaulting to False. If True, this will invert the x-axis and L and R annotations to confirm to radiological conventional view. (3172 by Konrad Wagstyl and Yasmin Mzayek).
  • Code Update Decoder objects to use the more efficient LogisticRegressionCV (3736 by Michelle Wang).
  • API Add LassoCV as a new estimator option for Decoder objects (3781 by Michelle Wang)
  • API Add vmin and symmetric_cbar arguments to ~nilearn.plotting.plot_img_on_surf (3873 by Michelle Wang).
  • API Improve contrasts allowing fixed effects on F contrasts (3203 by Bertrand Thirion)
  • API New experimental surface API to facilitate working with surface data in downstream surface-based analyses. We provide this API as a nilearn.experimental.surface module as it is still incomplete and subject to change without a deprecation cycle. (3856 by Jerome Dockes).

NEW

  • Plotting Volume plotting functions like ~plotting.plot_img now have an optional radiological parameter, defaulting to False. If True, this will invert the x-axis and L and R annotations to confirm to radiological conventional view. (3172 by Konrad Wagstyl and Yasmin Mzayek).
  • API New experimental surface API to facilitate working with surface data in downstream surface-based analyses. We provide this API as a nilearn.experimental.surface module as it is still incomplete and subject to change without a deprecation cycle. (3856 by Jerome Dockes).

Fixes

  • Code Fix bug in method transform_imgs of ~maskers.MultiNiftiMapsMasker and ~maskers.MultiNiftiLabelsMasker that would raise an error if a list of sample_mask was specified to fit_transform (3971 by Alexandre Cionca).
  • Plotting Fix bug in nilearn.plotting.surf_plotting._plot_surf_matplotlib that would make vertices transparent when saving in PDF or SVG format (3860 by Mathieu Dugré).
  • Plotting Fix bug that would prevent using symmetric_cmap=True or the avg_method argument with ~plotting.plot_surf_roi (3942 by Rémi Gau).
  • Code Fixes a bug that would lead to an error when loading a fsaverage surface while relying on numpy >= 1.24.x (3644 by Rémi Gau).
  • Code Fix bug that would prevent loading the confounds of a gifti file in actual fmriprep datasets (3819 by Rémi Gau).
  • Code Fix bug that prevented using dataframes as input for second level GLM when computing contrasts (3879 by Rémi Gau).
  • Code Fix bug in ~glm.first_level.first_level_from_bids that returned no confound files if the corresponding bold files contained derivatives BIDS entities (3742 by Rémi Gau).
  • Code Fix bug in ~glm.first_level.first_level_from_bids that would throw a warning about slice_time_ref not being provided even when it was (3811 by Rémi Gau).
  • Code Fix bug where the cv_params_ attribute of fitter Decoder objects sometimes had missing entries if grid_param is a sequence of dicts with different keys (3733 by Michelle Wang).
  • Code Make the ~nilearn.interfaces.fmriprep.load_confounds confounds file selection more generic (3794 by Taylor Salo).
  • Plotting Change default figure sizes to prevent titles from overlapping figure content (3797 by Yasmin Mzayek and see also 2804 by Oliver Warrington)
  • Code Relax the ~nilearn.interfaces.fmriprep.load_confounds confounds selection on cosine as not all confound files contained the variables (3816 by Hao-Ting Wang).
  • Code Fix pathlib.Path not being counted as Niimg-like object in ~image.new_img_like (3723 by Maximilian Cosmo Sitter).
  • Code Fix fit_transform behavior to match when fit method is passed image data (3897 by Yasmin Mzayek)
  • Plotting Allow using both vmin and threshold with "plotly" engine to be consistent with "matplotlib" behavior (3945 by Yasmin Mzayek)
  • Plotting Set edgecolors to be the same as facecolors in ~plotting.plot_surf_contours so that ROI contours are rendered clearly (3973 by Yasmin Mzayek)
  • API Refactor deprecation of behavior of ~datasets.fetch_atlas_craddock_2012, ~datasets.fetch_atlas_smith_2009 and ~datasets.fetch_atlas_basc_multiscale_2015 fetchers including using API consistent maps key (3987 by Yasmin Mzayek)

Enhancements

  • Doc Add cross-reference links to type definitions in public surface functions (3857 by Hao-Ting Wang).
  • Code Update Decoder objects to use the more efficient LogisticRegressionCV (3736 by Michelle Wang).
  • Code Throw warning in ~glm.first_level.first_level_from_bids when using event.tsv files with no trial type column (3597 by Aswin Vijayan, Rémi Gau).
  • API Make return key names in the description file of destrieux surface consistent with ~datasets.fetch_atlas_surf_destrieux (3774 by Tarun Samanta).
  • API Add LassoCV as a new estimator option for Decoder objects (3781 by Michelle Wang)
  • API Add vmin and symmetric_cbar arguments to ~nilearn.plotting.plot_img_on_surf (3873 by Michelle Wang).
  • API Improve generate_report method of maskers by allowing users to pass a cmap argument for plotting image (3897 by Yasmin Mzayek)
  • API Improve contrasts allowing fixed effects on F contrasts (3203 by Bertrand Thirion)

Changes

  • Code Validate the content of events files before plotting them (3994 by Rémi Gau).
  • Code nilearn.glm.first_level.experimental_paradigm.check_events will now throw a warning if some events have a 0 second duration and will throw an error if an event has NaN onset or duration (3943 by Rémi Gau).
  • Maint Removed old files and test code from deprecated datasets COBRE and NYU resting state (3743 by Michelle Wang).
  • Maint PEP8 and isort compliance extended to the whole nilearn codebase. (3538, 3566, 3548, 3556, 3601, 3609, 3646, 3650, 3647, 3640, 3615, 3614, 3648, 3651 by Rémi Gau).
  • Maint Finish applying black formatting to most of the codebase. (3836, 3833, 3827, 3810, 3803, 3802, 3795, 3790, 3783, 3777 by Rémi Gau).
  • Deprecation Empty region signals resulting from applying mask_img in ~maskers.NiftiLabelsMasker will no longer be kept in release 0.15. Meanwhile, use keep_masked_labels parameter when initializing the ~maskers.NiftiLabelsMasker object to enable/disable this behavior. (3722 by Mohammad Torabi).
  • Deprecation Empty region signals resulting from applying mask_img in ~maskers.NiftiMapsMasker will no longer be kept in release 0.15. Meanwhile, use keep_masked_maps parameter when initializing the ~maskers.NiftiMapsMasker object to enable/disable this behavior. (3732 by Mohammad Torabi).
  • Maint Removed mention of license in "header" (3838 by Czarina Sy).
  • Doc Configure plots in example gallery for better rendering (3753 by Yasmin Mzayek)
  • Maint Make one_mesh_info and full_brain_info into private functions _one_mesh_info and _full_brain_info (3847 by Rahul Brito)
  • Maint Refactor error raising tests using context managers (3854 BY François Paugam)
  • Deprecation Added warning to deprecate darkness in surf_plotting._compute_facecolors_matplotlib and html_surface._get_vertexcolor (:gh`3855` by Alisha Kodibagkar)
  • Doc Replace skipped doctests with default code-blocks (3681 in by Patrick Sadil)
  • Maint Move the ~nilearn.plotting.html_surface._mix_colormaps to cm.py in ~nilearn.plotting (3919 by Ahmad Chamma)
  • Maint Remove deprecation decorator from ~nilearn.glm.regression (3921 by Ahmad Chamma)
  • API Expose standardize in ~plotting.plot_carpet and ~connectome.ConnectivityMeasure to handle "zscore" deprecation (3927 by Yasmin Mzayek).
  • Doc Example sphx_glr_auto_examples_01_plotting_plot_prob_atlas.py is shortened to speed up build time (3934 by Yasmin Mzayek)