1 Release published by 1 person

• 0.11.0

  published Dec 2, 2024

41 Pull requests merged by 5 people

• [REF] simplify-len-comparison

  #4821 merged Dec 2, 2024

• [REF] Apply de Morgan's law for conditional

  #4831 merged Dec 2, 2024

• [REF] move assign variable within the if block where they are needed

  #4823 merged Dec 2, 2024

• [STY] apply US spelling

  #4707 merged Dec 2, 2024

• [FIX] use linebreaks in doc to avoid noqa

  #4815 merged Dec 2, 2024

• [REF] remove redundant slice index

  #4825 merged Dec 2, 2024

• [REF] apply use-fstring suggested by sourcery

  #4819 merged Dec 2, 2024

• [REF] apply sourcery suggestions to use comprehension

  #4822 merged Dec 2, 2024

• [REF] refactor unnecessary else block

  #4826 merged Dec 2, 2024

• [REF] use dict comprehension

  #4833 merged Dec 2, 2024

• [FIX] rendering version changed

  #4842 merged Dec 2, 2024

• [REF] avoid not any() or not all()

  #4843 merged Dec 2, 2024

• [REF] use join

  #4844 merged Dec 2, 2024

• [REF] simplify empty collection comparison

  #4845 merged Dec 2, 2024

• [REF] use underscore for unused variable in loop

  #4846 merged Dec 2, 2024

• Bump actions/checkout from 3 to 4

  #4850 merged Dec 2, 2024

• [FIX] update plot_localizer_surface_analysis

  #4840 merged Dec 2, 2024

• [FIX] update plot_surface_image_and_maskers.py

  #4835 merged Dec 2, 2024

• [FIX] update plot_surface_101 example

  #4834 merged Dec 2, 2024

• [FIX] update plot_surf_stat_map to properly use surface api

  #4838 merged Dec 2, 2024

• [FIX] update plot_3d_map_to_surface_projection

  #4837 merged Dec 2, 2024

• [FIX] update plot_surface_bids_analysis

  #4841 merged Dec 2, 2024

• [FIX] rework plot_surf_atlas example

  #4836 merged Dec 2, 2024

• [REL] 0.11.0

  #4813 merged Nov 29, 2024

• [ENH] fit second level model on surface

  #4715 merged Nov 29, 2024

• [DOC][FIX] update number of participants loaded in load_nki

  #4817 merged Nov 29, 2024

• [ENH] allow to ignore certain BIDS entities when using query_bids

  #4802 merged Nov 29, 2024

• [ENH] revert coercing surface data to 2D

  #4793 merged Nov 29, 2024

• [ENH] Remove old surface

  #4791 merged Nov 28, 2024

• [STY] Unused import

  #4812 merged Nov 28, 2024

• [FIX] Allow single 4D nifti as input for SecondLevelModel

  #4806 merged Nov 28, 2024

• [FIX] allow t_r, high_pass, low_pass to be int in signal.clean

  #4804 merged Nov 28, 2024

• [DOC] add bluesky to footer

  #4800 merged Nov 27, 2024

• [STY] Implicit enumerate calls

  #4799 merged Nov 27, 2024

• [DOC] move doc string for classes out of constructor

  #4795 merged Nov 27, 2024

• [MAINT] update checks scikit learn >= 1.7

  #4796 merged Nov 27, 2024

• [STY] Use .items() to iterate over the dictionary

  #4798 merged Nov 27, 2024

• [MAINT] increase coverage

  #4794 merged Nov 26, 2024

• [ENH] run GLM on surface data on BIDS datasets

  #4507 merged Nov 26, 2024

• [DOC] Fix render of lists, notes and code blocks in 'template' parameters

  #4790 merged Nov 26, 2024

• [ENH] make the number of vertices the first dimension of image data

  #4591 merged Nov 26, 2024

17 Pull requests opened by 5 people

• [FIX][ENH][DOC] allow events and design matrices inputs to be pathlike

  #4807 opened Nov 27, 2024

• [ENH] implement `strategy` for surface label masker

  #4809 opened Nov 27, 2024

• fix links

  #4814 opened Nov 28, 2024

• [STY] run style checks on doc

  #4818 opened Nov 29, 2024

• [WIP] generate look up tables for deterministic atlases

  #4820 opened Nov 29, 2024

• [REF] simplify assignement

  #4824 opened Nov 29, 2024

• [REF] use list extend instead of append

  #4827 opened Nov 29, 2024

• [REF] raise exception from previous error

  #4828 opened Nov 29, 2024

• [ENH] Implement surface maps masker

  #4830 opened Nov 29, 2024

• [REF] use get item where possible

  #4832 opened Nov 29, 2024

• [DOC] use higher contrast pygment style for dark mode

  #4847 opened Dec 1, 2024

• [FIX] add two_sided parameter to RegionExtractor

  #4849 opened Dec 2, 2024

• [DOC] update colormap example

  #4851 opened Dec 2, 2024

• [FIX] release_docs workflow

  #4854 opened Dec 2, 2024

• [FIX] Save gifti with datatype None

  #4857 opened Dec 2, 2024

• chore: update pre-commit hooks

  #4858 opened Dec 2, 2024

• [FIX] Addressing B028 Errors with Stacklevel Adjustmentso resolve B028 errors

  #4859 opened Dec 2, 2024

15 Issues closed by 1 person

• grey or gray? american or british english?

  #4700 closed Dec 2, 2024

• `# noqa` statements will show up in doc examples in future releases

  #4712 closed Dec 2, 2024

• support 2nd level GLM analysis of SurfaceImage objects

  #4617 closed Nov 29, 2024

• Revert coercing surface data to 2D

  #4792 closed Nov 29, 2024

• Roadmap 0.11.0

  #3812 closed Nov 28, 2024

• [META] Next steps for development on experimental surface module

  #4027 closed Nov 28, 2024

• [ENH] Move/remove/drop support for old surface-related stuff

  #4789 closed Nov 28, 2024

• Passing a 4D image to `SecondLevelModel`

  #3058 closed Nov 28, 2024

• Checks on t_r type too stringent in signals

  #4803 closed Nov 28, 2024

• `filter` option in `signal.clean` is not exposed to `nilearn.maskers.NiftiMasker` and potentially other masker objects

  #3437 closed Nov 27, 2024

• [DOC] inconsistent Doc style for classes

  #4633 closed Nov 27, 2024

• :rotating_light: NIGHTLY DEPENDENCIES TEST: failure on `refs/heads/main`

  #4769 closed Nov 27, 2024

• Adapt first_level_from_bids to run on surface images directly

  #4567 closed Nov 26, 2024

• What should be the shape of data in SurfaceImage?

  #4569 closed Nov 26, 2024

• `nilearn.input_data.fmriprep_confounds` not retrieving confound files correctly when entity `part-` is present

  #3020 closed Nov 26, 2024

12 Issues opened by 8 people

• [DOC] method `set_output` mentioned but not yet implemented

  #4856 opened Dec 2, 2024

• [BUG] Some new test failures on s390x (big-endian) in 0.11.0

  #4855 opened Dec 2, 2024

• update labels connectome in plot_surfac_image_maskers

  #4852 opened Dec 2, 2024

• change some of the default colormap used by nilearn

  #4848 opened Dec 1, 2024

• [ENH] Implement SurfaceMapsMasker to allow `Parcellations` to work with surface data

  #4829 opened Nov 29, 2024

• Rename examples

  #4816 opened Nov 29, 2024

• [ENH] avoid loading whole nifti-like image data when extracting time-series within a mask

  #4811 opened Nov 27, 2024

• [ENH] implement strategies in SurfaceLabelMasker

  #4810 opened Nov 27, 2024

• [ENH] `concat_imgs` should be able to concatenate surface images

  #4808 opened Nov 27, 2024

• [ENH] Add Tests to Better Cover the Cleaning Behavior of Maskers

  #4805 opened Nov 27, 2024

• Localizer BIDS dataset derivative not BIDS compliant

  #4801 opened Nov 27, 2024

• [FIX] Addressing B028 Errors with Stack Level Adjustments

  #4797 opened Nov 26, 2024

73 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• add the option to provide path to labels tsv

  #4767 commented on Nov 29, 2024 • 3 new comments

• [ENH] Allow `Parcellations` and `DictLearning` to work with Surface API

  #4756 commented on Nov 29, 2024 • 3 new comments

• [FIX] Fixed two-sided threshold

  #4501 commented on Nov 29, 2024 • 0 new comments

• [ENH] add bland-altman plots for image comparison

  #4089 commented on Nov 29, 2024 • 0 new comments

• plots in plot_second_level_association_test.py don't show any activation

  #3979 commented on Nov 29, 2024 • 0 new comments

• add region labels to coordinate tables of activation maps

  #3940 commented on Nov 29, 2024 • 0 new comments

• [MAINT] refactor complex and long functions

  #3655 commented on Nov 29, 2024 • 0 new comments

• [ENH] add a `.git-blame-ignore-revs` to ignore formatting PR from git blame

  #3653 commented on Nov 29, 2024 • 0 new comments

• Support missing regressors in FirstlevelGLM

  #2401 commented on Nov 29, 2024 • 0 new comments

• get_data (via load_niimg) casts to float64 (high memory usage)

  #2209 commented on Nov 29, 2024 • 0 new comments

• change the localizer condition identifiers

  #2386 commented on Nov 29, 2024 • 0 new comments

• Filtering does not work for `fetch_neurovault`

  #1700 commented on Nov 29, 2024 • 0 new comments

• restore link to artifacts in github PR pages

  #2508 commented on Nov 29, 2024 • 0 new comments

• Contours are wrapped to side of image if they coincide with the cut plane

  #1605 commented on Nov 29, 2024 • 0 new comments

• Parallelizing NiftiSpheres/LabelsMasker?

  #1501 commented on Nov 29, 2024 • 0 new comments

• [suggestions] When no labels are found with random walker in RegionExtractor

  #1245 commented on Nov 29, 2024 • 0 new comments

• `image.index_img` for the case of 3D volumes

  #1346 commented on Nov 29, 2024 • 0 new comments

• sklearn's GraphLassoCV or ConnectivityMeasure(cov_estimator=GraphLassoCV) ?

  #1213 commented on Nov 29, 2024 • 0 new comments

• find_xyz_cut_coords default thresholding fails for binary inputs if integer type

  #1194 commented on Nov 29, 2024 • 0 new comments

• Dataset downloading: handle dataset version

  #1039 commented on Nov 29, 2024 • 0 new comments

• [FIX] improve display in notebooks

  #4453 commented on Nov 29, 2024 • 0 new comments

• [DOC] Add comparison of meaning differences of GLM between different libraries

  #4287 commented on Nov 29, 2024 • 0 new comments

• [MAINT] Refactor image.resampling.resample_img

  #3701 commented on Nov 29, 2024 • 0 new comments

• [MAINT] refactor permuted_ols

  #3666 commented on Nov 29, 2024 • 0 new comments

• [ENH] Smoothing of surface data

  #3267 commented on Nov 29, 2024 • 0 new comments

• [WIP] PoSCE: population shrinkage of covariance estimator

  #1994 commented on Nov 29, 2024 • 0 new comments

• [BUG] RegionExtractor does not have a two-tailed behavior.

  #4409 commented on Dec 2, 2024 • 0 new comments

• Plotting flat maps + plotting additional data as transparency

  #2658 commented on Dec 1, 2024 • 0 new comments

• [BUG] `HierarchicalKMeans.fit()` takes transposed X

  #4755 commented on Nov 29, 2024 • 0 new comments

• Update internal documentation on how the Doc gets build and deployed.

  #4496 commented on Nov 29, 2024 • 0 new comments

• GLM method section

  #4493 commented on Nov 29, 2024 • 0 new comments

• report CSS and code refactor

  #4368 commented on Nov 29, 2024 • 0 new comments

• Fitted NiftiSphereMasker should contain a representation of the mask ?

  #4345 commented on Nov 29, 2024 • 0 new comments

• Passing negative values as threshold for plotting

  #4340 commented on Nov 29, 2024 • 0 new comments

• plot_matrix color bar not centered on "zero" when using a symmetric color bar

  #4293 commented on Nov 29, 2024 • 0 new comments

• refactor thresholding/masking to avoid duplication

  #4292 commented on Nov 29, 2024 • 0 new comments

• add `label (brain region)` and `maps (brain region)` (as defined in the user guide) as part of the nilearn glossary

  #4288 commented on Nov 29, 2024 • 0 new comments

• [DOC] todo of missing default value in docstrings

  #3865 commented on Nov 29, 2024 • 0 new comments

• [ENH] add transparency on visualization to display both beta and T values on the same visualization.

  #3789 commented on Nov 29, 2024 • 0 new comments

• [BUG] Improving brain atlases and standardize them

  #4335 commented on Nov 29, 2024 • 0 new comments

• failures to generate reports with several atlases

  #4331 commented on Nov 29, 2024 • 0 new comments

• destrieux atlas returns wrong region_names_

  #4330 commented on Nov 29, 2024 • 0 new comments

• Document that SurfaceImage cannot be loaded from a single file yet

  #4622 commented on Nov 29, 2024 • 0 new comments

• Set up a benchmark suite to assess performance and check for improvment or regression

  #4573 commented on Nov 29, 2024 • 0 new comments

• GLM report on surface

  #4566 commented on Nov 29, 2024 • 0 new comments

• use scikit-learn check_estimator to ensure compatibiity of Nilearn estimators with scikit-learn

  #4538 commented on Nov 29, 2024 • 0 new comments

• [ENH] add possibility to compute design efficiency for a design matrix and a given contrast (or set of contrasts)

  #4526 commented on Nov 29, 2024 • 0 new comments

• [ENH] Include "goodness of fit" image in GLM reports ?

  #4525 commented on Nov 29, 2024 • 0 new comments

• [ENH] The class FirstLevelModel should directly support the usage of Cifti files as input (dtseries)

  #4429 commented on Nov 29, 2024 • 0 new comments

• add `mask` or `mask_img` to SurfaceLabelsMasker

  #4759 commented on Nov 29, 2024 • 0 new comments

• [ENH] nilearn.plotting.view_surf for both hemispheres?

  #4664 commented on Nov 29, 2024 • 0 new comments

• [DOC] Use a proper surface dataset in surface Searchlight example

  #4717 commented on Nov 29, 2024 • 0 new comments

• Further refactoring of surface fixture

  #4686 commented on Nov 29, 2024 • 0 new comments

• [ENH] Include destrieux atlas a2009s with subcortical regions

  #4765 commented on Nov 28, 2024 • 0 new comments

• use pre-commit CI to run checks and update hooks

  #4760 commented on Nov 28, 2024 • 0 new comments

• NiftiMasker should not be used for unmasking list of niimg

  #1001 commented on Nov 29, 2024 • 0 new comments

• add_regs param of make_design_matrix() in design_matrix.py should handle the format of the passed in data transparently.

  #2379 commented on Nov 29, 2024 • 0 new comments

• Incomprehensible ValueError thrown by RegionExtractor

  #907 commented on Nov 29, 2024 • 0 new comments

• Simplify the LikelihoodModelResults.

  #2381 commented on Nov 29, 2024 • 0 new comments

• Improper parameter name & non-optimal args for atlas Pauli 2017

  #2239 commented on Nov 29, 2024 • 0 new comments

• [DOC] check new pages of the new surface API

  #4728 commented on Nov 29, 2024 • 0 new comments

• NiftiMasker mask_strategy generate wrong mask

  #3358 commented on Nov 29, 2024 • 0 new comments

• Deprecate bytes and metadata as numpy arrays in datasets

  #2660 commented on Nov 29, 2024 • 0 new comments

• Ease the use of NiftiMapsMasker on more than 10,000 images (3D)

  #1754 commented on Nov 29, 2024 • 0 new comments

• New functionality for nilearn.image.resample_img

  #1801 commented on Nov 29, 2024 • 0 new comments

• MemoryError while masking timecourse file using a mask at a higher resolution

  #1883 commented on Nov 29, 2024 • 0 new comments

• Iterate over big 4d niimages

  #719 commented on Nov 29, 2024 • 0 new comments

• Thresholding surface images

  #2747 commented on Nov 29, 2024 • 0 new comments

• plotting multiple stat maps on surface

  #3189 commented on Nov 29, 2024 • 0 new comments

• fsaverage as provided with FreeSurfer is not in MNI152 space but nilearn examples project data in MNI152 space onto it without any mentions of limitations or mitigations

  #3514 commented on Nov 29, 2024 • 0 new comments

• Smoothing function for surface data

  #2949 commented on Nov 29, 2024 • 0 new comments

• Cifti support

  #2388 commented on Nov 29, 2024 • 0 new comments

• [ENH] Nilearn plotting of RGB-type images

  #4224 commented on Nov 29, 2024 • 0 new comments