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nilearn

0.9.2

Released August 2022

HIGHLIGHTS

  • Updated docs with a new theme using furo (3125 by Alexis Thual).
  • ~mass_univariate.permuted_ols and ~glm.second_level.non_parametric_inference now support TFCE statistic (3196 by Taylor Salo).
  • ~mass_univariate.permuted_ols and ~glm.second_level.non_parametric_inference now support cluster-level Family-wise error correction (3181 by Taylor Salo).
  • ~interfaces.bids.save_glm_to_bids has been added, which writes model outputs to disk according to BIDS convention (2715 by Taylor Salo).

NEW

  • ~interfaces.bids.save_glm_to_bids has been added, which writes model outputs to disk according to BIDS convention (2715 by Taylor Salo).
  • ~mass_univariate.permuted_ols and ~glm.second_level.non_parametric_inference now support TFCE statistic (3196 by Taylor Salo).
  • ~mass_univariate.permuted_ols and ~glm.second_level.non_parametric_inference now support cluster-level Family-wise error correction (3181 by Taylor Salo).
  • Updated docs with a new theme using furo (3125 by Alexis Thual).

Fixes

  • Fix _NEUROVAULT_BASE_URL and _NEUROSYNTH_FETCH_WORDS_URL in nilearn/datasets/neurovault.py by using https instead of http (3281 by Manon Pietrantoni).
  • Convert references in nilearn/mass_univariate/permuted_least_squares.py to use bibtex format (3222 by Yasmin Mzayek).
  • Update Craddock 2012 parcellation url in nilearn/datasets/atlas.py (3233 by Vasco Diogo)
  • ~plotting.plot_roi failed before when used with the "contours" view type and passing a list of cut coordinates in display mode "x", "y" or "z"; this has been corrected (3241 by Jerome Dockes).
  • ~plotting.plot_markers can now plot a single scatter point (3255 by Caglar Cakan).
  • Fix title display for ~plotting.plot_surf_stat_map. The title argument does not set the figure title anymore but the axis title. (3220 by Raphael Meudec).
  • ~surface.load_surf_mesh loaded FreeSurfer specific surface files (e.g. .pial) with a shift in the coordinates. This is fixed by adding the c_ras coordinates to the mesh coordinates (3235 by Yasmin Mzayek).
  • Function nilearn.glm.second_level.second_level._check_second_level_input now raises an error when flm_object argument is False and second_level_input is a list of ~glm.first_level.FirstLevelModel (3283 by Matthieu Joulot).
  • Function ~image.resample_img now warns the user if the provided image has an sform code equal to 0 or None (3284 by Matthieu Joulot).
  • Fix usage of scipy.stats.gamma.pdf in _gamma_difference_hrf function under nilearn/glm/first_level/hemodynamic_models.py, which resulted in slight distortion of HRF (3297 by Kun CHEN).
  • Fix bug introduced due to a fix in the pre-release version of scipy (1.9.0rc1) which now enforces that elements of a band-pass filter must meet condition Wn[0] < Wn[1]. Now if band-pass elements are equal ~nilearn.signal.butterworth returns an unfiltered signal with a warning (3293 by Yasmin Mzayek).
  • The parameter alpha is now correctly passed to ~plotting.plot_glass_brain in ~plotting.plot_connectome (3306 by Koen Helwegen).
  • Fix plotting of background image in ~nilearn.plotting.view_img when the background is not the MNI template (3312 by Jerome Dockes).
  • Fix the typographic error on the page sphx_glr_auto_examples_04_glm_first_level_plot_adhd_dmn.py (3337 by Sachin Patalasingh).

Enhancements

  • Add sample_masks to ~glm.first_level.FirstLevelModel.fit for censoring time points (3193 by Hao-Ting Wang).
  • Function ~glm.first_level.run_glm and class ~glm.first_level.FirstLevelModel now accept a random_state parameter, which allows users to seed the KMeans cluster model used to estimate AR coefficients. (3185 by Sami Jawhar).
  • Conform seeding and docstrings in module _utils.data_gen (3262 by Yasmin Mzayek).
  • Docstrings of module ~nilearn.glm.second_level were improved (3030 by Nicolas Gensollen).
  • In ~reporting.get_clusters_table, when the center of mass of a binary cluster falls outside the cluster, report the nearest within-cluster voxel instead (3292 by Connor Lane).
  • Add n_elements_ attribute to masker classes (3311 by Taylor Salo).
  • Functions expecting string filesystem paths now also accept path-like objects (3300 by Yasmin Mzayek).
  • Contributing guidelines now include a recommendation to run flake8 locally on the branch diff with main (3317 by Yasmin Mzayek).
  • Improvements to ~mass_univariate.permuted_ols and ~glm.second_level.non_parametric_inference with TFCE statistic runtime (3333 by Sage Hahn).
  • ~maskers.NiftiLabelsMasker now accepts 1-dimensional arrays in its ~maskers.NiftiLabelsMasker.inverse_transform method (3322 by Taylor Salo).

Changes

  • Function ~plotting.plot_carpet argument cmap now respects behaviour specified by docs and changes the color of the carpet_plot. Changing the label colors is now delegated to a new variable cmap_labels (3209 by Daniel Gomez).
  • Function ~datasets.fetch_surf_fsaverage no longer supports the previously deprecated option fsaverage5_sphere (3229 by Taylor Salo).
  • Classes ~glm.regression.RegressionResults, ~glm.regression.SimpleRegressionResults, ~glm.regression.OLSModel, and ~glm.model.LikelihoodModelResults no longer support deprecated shortened attribute names, including df_resid, wdesign, wresid, norm_resid, resid, and wY (3229 by Taylor Salo).
  • Function ~datasets.fetch_openneuro_dataset_index is now deprecated in favor of the new ~datasets.fetch_ds000030_urls function (3216 by Taylor Salo).
  • 64-bit integers in Nifti files: some tools such as FSL, SPM and AFNI cannot handle Nifti images containing 64-bit integers. To avoid compatibility issues, it is best to avoid writing such images and in the future trying to create them with nibabel without explicitly specifying a data type will result in an error. See details in this issue: nipy/nibabel#1046 and this PR: nipy/nibabel#1082. To avoid this, ~image.new_img_like now warns when given int64 arrays and converts them to int32 when possible (ie when it would not result in an overflow). Moreover, any atlas fetcher that returned int64 images now produces images containing smaller ints. (3227 by Jerome Dockes)
  • Refactors fmriprep confound loading such that that the parsing of the relevant image file and the loading of the confounds are done in separate steps (3274 by David G Ellis).
  • Private submodules, functions, and classes from the ~nilearn.decomposition module now start with a "_" character to make it clear that they are not part of the public API (3141 by Nicolas Gensollen).
  • Convert references in nilearn/glm/regression.py and nilearn/glm/thresholding.py to use footcite/footbibliography (3302 by Ahmad Chamma).
  • Boolean input data in ~image.new_img_like now defaults to np.uint8 instead of np.int8 (3286 by Yasmin Mzayek).
  • The current behavior of maskers' transform on 3D niimg inputs, in which a 2D array is returned, is deprecated, and 1D arrays will be returned starting in version 0.12 (3322 by Taylor Salo).