Released November 2024

List of pull requests

• [MAINT] Post release 0.10.4 by @Remi-Gau in #4366
• [MAINT] clean up makefiles and allow color in CLI in github workflows by @Remi-Gau in #4370
• [DOC] update release procotol by @Remi-Gau in #4371
• Change "resting state" to "movie watching" in compare means example by @man-shu in #4373
• [DOC] Mention in style guide the meaning of trailing underscore for attributes by @Remi-Gau in #4374
• [REF] Refactor CSS and html masker reports by @Remi-Gau in #4372
• [BOT] update pre-commit hooks by @github-actions in #4381
• [FIX] skip problematic plotting in doc build by @Remi-Gau in #4383
• [ENH] enhance save_glm_to_bids outputs by @Remi-Gau in #4375
• [MAINT] change schedule of GH workflows by @Remi-Gau in #4386
• [MAINT] monitor duration of doc build by @Remi-Gau in #4387
• [MAINT] pre-download data on full doc build by @Remi-Gau in #4390
• [FIX] fix flake8 bugbear errors by @Remi-Gau in #4384
• [MAINT] improve workflow to test on nightly dependencies by @Remi-Gau in #4364
• [MAINT] update precommit configuration by @Remi-Gau in #4391
• [MAINT] update parameters for scipy.sparse.linalg.cg by @Remi-Gau in #4394
• [FIX] remove, implement or better document "unused" arguments by @Remi-Gau in #4273
• [MAINT] Update circle-ci trigger-hosting by @Remi-Gau in #4402
• [REF] refactor style checks in CI by @Remi-Gau in #4406
• [MAINT] test on several macos versions by @Remi-Gau in #4405
• [DOC] Fix typos found by codespell by @DimitriPapadopoulos in #4410
• FIX failing load_confound test related to standardisation by @htwangtw in #4411
• add width input to view_img() by @alexsayal in #4416
• [BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in #4418
• [FIX] Raise error if unknown kwargs are given to first_level_from_bids by @michellewang in #4414
• [FIX] Refactor design matrix and contrast formula for the two-sample T-test example by @YCHuang0610 in #4407
• [BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in #4422
• [MAINT] only on use macOS-latest by @Remi-Gau in #4424
• [MAINT] pacify codepspell by @Remi-Gau in #4430
• [ENH] add plotting functions to the experimental surface module by @jeromedockes in #4235
• [ENH] Adapt FirstLevelModel to work with surface data objects from new API by @ymzayek in #4126
• Copy input image header to the output by default by @man-shu in #4397
• Example to demonstrate copy_header_from in math_img by @man-shu in #4392
• [STY] apply black to files no longer invovled in other pull requests by @Remi-Gau in #4433
• [ENH] Add warning for future change of the default of force_resample to True by @ajoshiusc in #4412
• [MAINT] remove some try/except on imports by @Remi-Gau in #4440
• [ENH] add footer to all masker reports by @Remi-Gau in #4307
• [ENH] expand surface plotting with new surface object by @Remi-Gau in #4431
• [ENH] update example to show parametric modulation by @Remi-Gau in #4436
• [MAINT] add force_resample where missing by @Remi-Gau in #4441
• [DOC] add ...CV in logistic estimator name by @man-shu in #4438
• [BOT] update pre-commit hooks by @github-actions in #4447
• [REF] add force_resample default to cached calls by @Remi-Gau in #4450
• [ENH] add report for SurfaceMasker by @Remi-Gau in #4432
• [MAINT] remove duplicate code by @Remi-Gau in #4449
• [DOC] Fix deploy doc on main by @Remi-Gau in #4455
• [REF] minor refactor of get_cmap and matplotlib version-handling by @Remi-Gau in #4458
• [REF] refactor report templates by @Remi-Gau in #4460
• [FIX] throw warning a masker generate_report is called without matplotlib by @Remi-Gau in #4457
• [FIX] use string as label names in example involving the new surface based destrieux atlas by @Remi-Gau in #4462
• [REF] refactor FLM fitting by @Remi-Gau in #4461
• [MAINT] for monitoring of duration of CI only plot doc build on main (full builds) by @Remi-Gau in #4463
• [MAINT] rename tr variable - private occurences by @Remi-Gau in #4468
• [ENH] Replace tr by t_r in HRF generating functions and examples by @Remi-Gau in #4470
• [FIX] pacify ruff warning about numpy 2 by @Remi-Gau in #4477
• [FIX] coerce loaded data from NKI to float in examples by @Remi-Gau in #4475
• [ENH] add function to plot regressor correlation matrix by @Remi-Gau in #4467
• [ENH] use nilearn logger.log function instead of print or sys.stderr.write by @Remi-Gau in #4469
• [FIX] change creation of region_names and add test by @mtorabi59 in #4360
• [FIX] fix trigger hosting of doc of PR on circle-ci by @Remi-Gau in #4481
• [FIX] Change default ratio value in glover to fit canonical Glover HRF (1999) by @const7 in #4452
• Update second_level.py by @arovai in #4483
• [MAINT] use pytest-reporter-html1 to create test reports by @Remi-Gau in #4444
• Revert "[MAINT] use pytest-reporter-html1 to create test reports" by @Remi-Gau in #4485
• [BOT] update pre-commit hooks by @github-actions in #4487
• [FIX] host doc from PR on Circle-CI by @Remi-Gau in #4494
• Explain Decoder's default cross-validation scheme by @man-shu in #4491
• Change default clustering_percentile in _BaseDecoder docstring by @man-shu in #4489
• [BOT] update pre-commit hooks by @github-actions in #4499
• [DOC] Small correction on instructions for setting up environment by @kimsin98 in #4459
• [API] renamed ax parameter for consistency by @muddi900 in #4476
• [BOT] update AUTHORS.rst and doc/changes/names.rst by @github-actions in #4504
• [FIX] Reduce dtype of mask from int64 to int8 in image.binarize_img by @psadil in #4502
• [FIX] force np.float64 format for second level matrix dataframe by @Remi-Gau in #4503
• [MAINT] Finish adding tests for _utils.data_gen by @kimsin98 in #4465
• [REF] refactor nibabel import by @Remi-Gau in #4506
• [ENH] improve I/O for SurfaceImage by @Remi-Gau in #4446
• [FIX] revert save analyze for SPM auditory data by @Remi-Gau in #4508
• [MAINT] use pytest-reporter-html1 to create test reports by @Remi-Gau in #4486
• [BOT] update pre-commit hooks by @github-actions in #4514
• [ENH] Change Butterworth filtering in nilearn.signal.clean to use 'sos' output by @Remi-Gau in #4510
• [STY] apply black to remaining example by @Remi-Gau in #4518
• [STY] apply black to remaining files in plotting subpackage by @Remi-Gau in #4520
• [STY] apply black to surface subpackage by @Remi-Gau in #4519
• [REF] remove obsolete try import by @Remi-Gau in #4528
• [MAINT] Handle 2 numpy and matplolib deprecation warnings by @Remi-Gau in #4522
• [MAINT] raise stacklevel of copy_header warning ...

Released April 2024

HIGHLIGHTS

• Use the appropriate HTML templates for nilearn.maskers.MultiNiftiMapsMasker and nilearn.maskers.MultiNiftiLabelsMasker reports that would lead to empty reports for MultiNiftiMapsMasker (#4310 by Rémi Gau).

• Fix color bar handling with color map with only 1 level (#4255 by Rémi Gau).

• Improve colorbar size and labels in mosaic display (#4284 by Rémi Gau).

• Remove unused **kwargs from nilearn.plotting.view_img and nilearn.plotting.plot_surf (#4270 by Rémi Gau).

Fixes

• Fix plotting of carpet plot due to a change in the coming version of matplolib (3.9.0) (#4279 by Rémi Gau).

• Fix errant warning when using stat_type in nilearn.glm.compute_contrast (#4257 by Eric Larson).

• Fix when thresholding is applied to images by GLM reports (#4258 by Rémi Gau).

• Use the appropriate HTML templates for nilearn.maskers.MultiNiftiMapsMasker and nilearn.maskers.MultiNiftiLabelsMasker reports that would lead to empty reports for MultiNiftiMapsMasker (#4310 by Rémi Gau).

• Make masker report tables horizontally scrollable (#4308 by Rémi Gau).-

• Masker reports tables do not overlap with report image (#4308 by Rémi Gau).

• Fix color bar handling with color map with only 1 level (#4255 by Rémi Gau).

• Ensure that region_names_ can be generated by nilearn.maskers.NiftiSpheresMasker.transform_single_imgs for deterministic atlases that use floats or non-consecutive values as region_ids whether they include background in their labels or not (#4274 by Rémi Gau).

• Ensure that nilearn.interfaces.bids.save_glm_to_bids serializes numpy arrays to list used as GLM parameters before saving them to JSON (#4325 by Rémi Gau).

• Check that the view parameter in surface plotting functions is a pair of int or float when it is not a string (#4297 by Rémi Gau).

• Fix positions of the markers on the images on the sphere masker reports (#4285 by Rémi Gau).

• Fix cut position in nifti maps maskers to match displayed map maximum (#4304 by Rémi Gau).

• Make sure that nilearn.maskers.NiftiSpheresMasker reports displays properly when it contains only 1 sphere (#4269 by Rémi Gau).

• Miscellaneous fixes in GLM reports (only display FIR delay if FIR is used, display color bar “Z score” legend…) (#4266 by Rémi Gau).

• Fix minor typos in documentation (glossary and connectivity/parcellating) (#4343 by Florent Pollet).

• Update minor information on the Code of Conduct page (#4318 and #4320 by Himanshu Aggarwal).

Enhancements

• Add an avg_method parameter to nilearn.plotting.plot_surf_stat_map (#4298 by Rémi Gau).

• Advertise nilearn’s in built globbing capability in an example (#4334 by Himanshu Aggarwal).

Changes

• Throw warnings when passing parameters to surface plotting functions that are not used by the plotly engine (#4298 by Rémi Gau).

• Improve colorbar size and labels in mosaic display (#4284 by Rémi Gau).

• Change the colormap to gray for the background image in the nilearn.maskers.NiftiSpheresMasker (#4269 by Rémi Gau).

• Remove unused **kwargs from nilearn.plotting.view_img and nilearn.plotting.plot_surf (#4270 by Rémi Gau).

• Use red to blue color map in the GLM reports (#4266 by Rémi Gau).

• nilearn.maskers.NiftiSpheresMasker will throw warnings if the labels passed to it is not a list of str, or if the number of items in the list of labels does not match the number of regions in the label image (#4274 by Rémi Gau).

• Copy headers from user-specified image to the result of nilearn.image.math_img (#4337 by Himanshu Aggarwal).

• Render the description of the templates, atlases and datasets of the nilearn.datasets as part of the documentation (#4232 by Rémi Gau).

• Render examples of GLM and masker reports as part of the documentation (#4267 and #4295 by Rémi Gau).

• HTML, CSS are now linted using prettier. (#4302, by Rémi Gau).

List of pull requests

• [MAINT] Post release 0.10.3 by @Remi-Gau in #4246
• [MAINT] Refactor test reporting by @Remi-Gau in #4247
• [MAINT] remove date from copyright by @Remi-Gau in #4249
• [FIX] numpy 2 compatibility by @Remi-Gau in #4251
• [DOC] Add datasets description to the documentation by @Remi-Gau in #4232
• [FIX] Replace remaining contrast_type by stat_type by @larsoner in https://github.com/nilearn/nil...

Released January 2024

HIGHLIGHTS

• API Allow passing arguments to first_level_from_bids to build first level models that include specific set of confounds by relying on the strategies from load_confounds (#4103 by Rémi Gau).

• Support passing t and F contrasts to compute_contrast that that have fewer columns than the number of estimated parameters. Remaining columns are padded with zero (#4067 by Rémi Gau).

• NiftiSpheresMasker now has generate_report method (#3102 by Yasmin Mzayek and Nicolas Gensollen).

• Update the CompCor strategy in load_confounds and load_confounds_strategy to support fmriprep 21.x series and above. (#3285 by Hao-Ting Wang).

• Allow setting vmin in plot_glass_brain and plot_stat_map (#3993 by Michelle Wang).

• 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).

• 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).

NEW

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

Fixes

• MultiNiftiMasker can now call generate_report which will generate a report for the first subject in the list of subjects (#4001 by Yasmin Mzayek).

• Make sure that all atlases and datasets fetchers return a description (#4215 Rémi Gau).

• Update the CompCor strategy in load_confounds and load_confounds_strategy to support fmriprep 21.x series and above. (#3285 by Hao-Ting Wang).

• Fix SimpleRegressionResults to accommodate for the lack of a model attribute (#4071 Rémi Gau)

• 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).

• 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 signal (#4116 by Hao-Ting Wang and Yasmin Mzayek).

• Fixed inheritance of decoder classes to keep compatibility with scikit-learn>v1.3 (#4188 by Yasmin Mzayek).

• Make sure that all the fetchers for atlas and func from nilearn.datasets return a sklearn.utils.Bunch. Add new behavior to 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

• NiftiSpheresMasker now has generate_report method (#3102 by Yasmin Mzayek and Nicolas Gensollen).

• Allow passing Pandas Series of image filenames to SecondLevelModel (#4070 by Rémi Gau).

• Allow passing arguments to first_level_from_bids to build first level models that include specific set of confounds by relying on the strategies from load_confounds (#4103 by Rémi Gau).

• Support passing t and F contrasts to compute_contrast that that have fewer columns than the number of estimated parameters. Remaining columns are padded with zero (#4067 by Rémi Gau).

• 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).

• Allow global_signal parameter in load_confounds_strategy in denoise_strategy='compcor' (#4225 by Hao-Ting Wang).

• Add two_sided option for binarize_img (#4121 by Steven Meisler).

• generate_report now uses appropriate cut coordinates when functional image is provided (#4099 by Yasmin Mzayek and Nicolas Gensollen).

• Mention the classification type (all-vs-one) in Decoding of a dataset after GLM fit for signal extraction (#4122 by Tamer Gezici).

• Add backslash to homogenize [Parcellations](https://nilearn.github.io/dev/modules/generated/nilearn.regions....

Released September 2023

HIGHLIGHTS

• 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..
• Update Decoder objects to use the more efficient LogisticRegressionCV.
• Add LassoCV as a new estimator option for Decoder objects
• Add vmin and symmetric_cbar arguments to nilearn.plotting.plot_img_on_surf.
• Improve contrasts allowing fixed effects on F contrasts
• 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..

NEW

• 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..
• 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..

Fixes

• 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.
• Fix bug in nilearn.plotting.surf_plotting._plot_surf_matplotlib that would make vertices transparent when saving in PDF or SVG format.
• Fix bug that would prevent using symmetric_cmap=True or the avg_method argument with plotting.plot_surf_roi.
• Fixes a bug that would lead to an error when loading a fsaverage surface while relying on numpy >= 1.24.x.
• Fix bug that would prevent loading the confounds of a gifti file in actual fmriprep datasets.
• Fix bug that prevented using dataframes as input for second level GLM when computing contrasts.
• Fix bug in glm.first_level.first_level_from_bids that returned no confound files if the corresponding bold files contained derivatives BIDS entities.
• 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.
• 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.
• Make the nilearn.interfaces.fmriprep.load_confounds confounds file selection more generic.
• Change default figure sizes to prevent titles from overlapping figure content
• Relax the nilearn.interfaces.fmriprep.load_confounds confounds selection on cosine as not all confound files contained the variables.
• Fix pathlib.Path not being counted as Niimg-like object in image.new_img_like.
• Fix fit_transform behavior to match when fit method is passed image data
• Allow using both vmin and threshold with "plotly" engine to be consistent with "matplotlib" behavior
• Set edgecolors to be the same as facecolors in plotting.plot_surf_contours so that ROI contours are rendered clearly
• 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

Enhancements

• Add cross-reference links to type definitions in public surface functions.
• Update Decoder objects to use the more efficient LogisticRegressionCV.
• Throw warning in glm.first_level.first_level_from_bids when using event.tsv files with no trial type column.
• Make return key names in the description file of destrieux surface consistent with datasets.fetch_atlas_surf_destrieux.
• Add LassoCV as a new estimator option for Decoder objects
• Add vmin and symmetric_cbar arguments to nilearn.plotting.plot_img_on_surf.
• Improve generate_report method of maskers by allowing users to pass a cmap argument for plotting image
• Improve contrasts allowing fixed effects on F contrasts

Changes

• Validate the content of events files before plotting them.
• 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.
• Removed old files and test code from deprecated datasets COBRE and NYU resting state.
• PEP8 and isort compliance extended to the whole nilearn codebase..
• Finish applying black formatting to most of the codebase..
• 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..
• 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..
• Removed mention of license in "header".
• Configure plots in example gallery for better rendering
• Make one_mesh_info and full_brain_info into private functions _one_mesh_info and _full_brain_info
• Refactor error raising tests using context managers
• Added warning to deprecate darkness in surf_plotting._compute_facecolors_matplotlib and html_surface._get_vertexcolor
• Replace skipped doctests with default code-blocks
• Move the ~nilearn.plotting.html_surface._mix_colormaps to cm.py in nilearn.plotting
• Remove deprecation decorator from ~nilearn.glm.regression
• Expose standardize in plotting.plot_carpet and connectome.ConnectivityMeasure to handle "zscore" deprecation.
• Example :ref:sphx_glr_auto_examples_01_plotting_plot_prob_atlas.py is shortened to speed up build time

List of pull requests

• Post release 0.10.1 by @ymzayek in #3730
• [MAINT] Format nilearn/plotting: apply isort and fix flake8 errors by @Remi-Gau in #3648
• [BOT] update pre-commit hooks by @github-actions in #3731
• [BOT] update pre-commit hooks by @github-actions in #3734
• [FIX] Missing values in Decoder.cv_params_ when param_grid is a list of dicts with different keys by @michellewang in #3733
• Correcting typo in the "load_confounds_strategy" function ("scrubbing") by @jonasmago in #3738
• [DOC] Fix broken doc build by @ymzayek in #3744
• [MAINT] Clean up remaining files from deprecated datasets (cobre, nyu) by @michellewang in #3743
• [ENH] Use LogisticRegressionCV instead of LogisticRegression to improve Decoder performance by @michellewang in #3736
• [FIX] Fix tests failing due to deprecations in pre-release dependencies by @ymzayek in #3746
• [INFRA] Add timeout setting in Azure Pipelines CI by @ymzayek in #3747
• [BOT] update pre-commit hooks by @github-actions in #3748
• add more info to adhd example by @mtorabi59 in #3739
• [MAINT] improve test coverage BaseMasker by @Remi-Gau in #3721
• [MAINT] refactor nilearn/maskers (sourcery, f-strings) by @Remi-Gau in #3685
• [MAINT] avoid creating files during testing: test_infer_effect_maps by @Remi-Gau in #3716
• [MAINT] Catch warnings as errors on partial doc builds by @ymzayek in #3749
• [FIX] force ordered output of _sanitize_reorder to match regex in test by @Remi-Gau in #3751
• [MAINT] run isort and flake8 on the whole nilearn code base in CI by @Remi-Gau in #3651
• [FIX] find confounds even when BIDS derivatives bold files contain res or den entities by @Remi-Gau in #3742
• [BOT] update pre-commit hooks by @github-actions in #3764
• [DOC] update changelog and git blame ignore by @Remi-Gau in #3755
• [FIX] Change error string to match scikit-learn InvalidParameterError message by @ymzayek in #3763
• [MAINT] relax regex for warning on sanitize reorder error by @Remi-Gau in #3766
• [DOC] fix duplicate entry in examples dropdown by @Remi-Gau in #3760
• [MAINT] refactor nilearn/datasets (sourcery, f-strings) by @Remi-Gau in #3727
• [MAINT] add workflow to check for f strings by @Remi-Gau in #3759
• [DOC] Remove license and hide authors in examples by @Remi-Gau in #3765
• [MAINT] refactor nilearn/plotting (f-strings) by @Remi-Gau in #3757
• [MAINT] remove test install with python 2.7 workflow by @Remi-Gau in #3768
• [REF] fix f strings by @Remi-Gau in #3770
• [ENH][DOC] Fix inconsistent description of return keys for fetch_atlas_surf_destrieux by @tarunsamanta2k20 in https://git...