├── .github ├── CODEOWNERS ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── development_todo_list.md │ ├── feature_request.md │ └── support-request.md └── workflows │ ├── github_actions_ci.yml │ ├── python_coverage.yml │ └── tagged_release.yml ├── .gitignore ├── BrainSpace.mltbx ├── BrainSpace.prj ├── CHANGELOG.txt ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── README.rst ├── brainspace ├── __init__.py ├── _version.py ├── datasets │ ├── __init__.py │ ├── base.py │ ├── matrices │ │ ├── fusion_tutorial │ │ │ └── vosdewael_200_mpc_matrix.csv │ │ ├── holdout_group │ │ │ ├── schaefer_100_mean_connectivity_matrix.csv │ │ │ ├── schaefer_200_mean_connectivity_matrix.csv │ │ │ ├── schaefer_300_mean_connectivity_matrix.csv │ │ │ ├── schaefer_400_mean_connectivity_matrix.csv │ │ │ ├── vosdewael_100_mean_connectivity_matrix.csv │ │ │ ├── vosdewael_200_mean_connectivity_matrix.csv │ │ │ ├── vosdewael_300_mean_connectivity_matrix.csv │ │ │ └── vosdewael_400_mean_connectivity_matrix.csv │ │ ├── individual │ │ │ ├── HCP_111009_maximum_vosdewael_300.csv │ │ │ ├── HCP_123824_median_vosdewael_300.csv │ │ │ ├── HCP_124624_maximum_schaefer_300.csv │ │ │ ├── HCP_124624_minimum_schaefer_200.csv │ │ │ ├── HCP_142828_minimum_schaefer_400.csv │ │ │ ├── HCP_144125_maximum_schaefer_100.csv │ │ │ ├── HCP_149236_maximum_vosdewael_200.csv │ │ │ ├── HCP_149236_minimum_vosdewael_100.csv │ │ │ ├── HCP_151425_median_vosdewael_400.csv │ │ │ ├── HCP_153025_minimum_vosdewael_400.csv │ │ │ ├── HCP_169949_median_schaefer_400.csv │ │ │ ├── HCP_175540_minimum_schaefer_300.csv │ │ │ ├── HCP_188347_maximum_schaefer_200.csv │ │ │ ├── HCP_208024_median_vosdewael_100.csv │ │ │ ├── HCP_246133_maximum_vosdewael_100.csv │ │ │ ├── HCP_275645_maximum_schaefer_400.csv │ │ │ ├── HCP_387959_maximum_vosdewael_400.csv │ │ │ ├── HCP_393247_minimum_schaefer_100.csv │ │ │ ├── HCP_393247_minimum_vosdewael_200.csv │ │ │ ├── HCP_395251_median_schaefer_200.csv │ │ │ ├── HCP_784565_median_vosdewael_200.csv │ │ │ ├── HCP_899885_median_schaefer_100.csv │ │ │ ├── HCP_958976_median_schaefer_300.csv │ │ │ └── HCP_958976_minimum_vosdewael_300.csv │ │ └── main_group │ │ │ ├── conte69_32k_curvature.csv │ │ │ ├── conte69_32k_fc_gradient0.csv │ │ │ ├── conte69_32k_fc_gradient1.csv │ │ │ ├── conte69_32k_mpc_gradient0.csv │ │ │ ├── conte69_32k_mpc_gradient1.csv │ │ │ ├── conte69_32k_t1wt2w.csv │ │ │ ├── conte69_32k_thickness.csv │ │ │ ├── schaefer_100_mean_connectivity_matrix.csv │ │ │ ├── schaefer_200_mean_connectivity_matrix.csv │ │ │ ├── schaefer_300_mean_connectivity_matrix.csv │ │ │ ├── schaefer_400_mean_connectivity_matrix.csv │ │ │ ├── vosdewael_100_mean_connectivity_matrix.csv │ │ │ ├── vosdewael_200_mean_connectivity_matrix.csv │ │ │ ├── vosdewael_300_mean_connectivity_matrix.csv │ │ │ └── vosdewael_400_mean_connectivity_matrix.csv │ ├── parcellations │ │ ├── mesulam_conte69.csv │ │ ├── schaefer_1000_conte69.csv │ │ ├── schaefer_100_conte69.csv │ │ ├── schaefer_200_conte69.csv │ │ ├── schaefer_300_conte69.csv │ │ ├── schaefer_400_conte69.csv │ │ ├── vosdewael_100_conte69.csv │ │ ├── vosdewael_200_conte69.csv │ │ ├── vosdewael_300_conte69.csv │ │ └── vosdewael_400_conte69.csv │ ├── preprocessing │ │ ├── sub-010188_ses-02_task-rest_acq-AP_run-01.fsa5.lh.mgz │ │ ├── sub-010188_ses-02_task-rest_acq-AP_run-01.fsa5.rh.mgz │ │ └── sub-010188_ses-02_task-rest_acq-AP_run-01_confounds.txt │ └── surfaces │ │ ├── conte69_32k_lh.gii │ │ ├── conte69_32k_lh_mask.csv │ │ ├── conte69_32k_lh_sphere.gii │ │ ├── conte69_32k_lh_temporal_mask.csv │ │ ├── conte69_32k_rh.gii │ │ ├── conte69_32k_rh_mask.csv │ │ ├── conte69_32k_rh_sphere.gii │ │ ├── conte69_32k_rh_temporal_mask.csv │ │ ├── fsa5.pial.lh.gii │ │ └── fsa5.pial.rh.gii ├── examples │ ├── README.txt │ ├── __init__.py │ ├── plot_tutorial0.py │ ├── plot_tutorial1.py │ ├── plot_tutorial2.py │ └── plot_tutorial3.py ├── gradient │ ├── __init__.py │ ├── alignment.py │ ├── embedding.py │ ├── gradient.py │ ├── kernels.py │ └── utils.py ├── mesh │ ├── __init__.py │ ├── array_operations.py │ ├── mesh_cluster.py │ ├── mesh_correspondence.py │ ├── mesh_creation.py │ ├── mesh_elements.py │ ├── mesh_io.py │ └── mesh_operations.py ├── null_models │ ├── __init__.py │ ├── moran.py │ ├── spin.py │ └── variogram.py ├── plotting │ ├── __init__.py │ ├── base.py │ ├── colormaps.py │ ├── defaults_plotting.py │ ├── sphinx_gallery_scrapper.py │ ├── surface_plotting.py │ ├── utils.py │ └── utils_qt.py ├── tests │ ├── __init__.py │ ├── test_alignment_methods.py │ ├── test_alignment_options.py │ ├── test_datasets.py │ ├── test_gradient.py │ ├── test_issue_133.py │ ├── test_mesh.py │ ├── test_null_models.py │ ├── test_parcellation.py │ ├── test_plotting.py │ ├── test_vtk94_compatibility.py │ └── test_wrapping.py ├── utils │ ├── __init__.py │ └── parcellation.py └── vtk_interface │ ├── __init__.py │ ├── checks.py │ ├── decorators.py │ ├── io_support │ ├── __init__.py │ ├── freesurfer_support.py │ └── gifti_support.py │ ├── pipeline.py │ └── wrappers │ ├── __init__.py │ ├── actor.py │ ├── algorithm.py │ ├── base.py │ ├── data_object.py │ ├── lookup_table.py │ ├── misc.py │ ├── property.py │ ├── renderer.py │ └── utils.py ├── docs ├── Makefile ├── _static │ └── getting_started00.png ├── conf.py ├── index.rst ├── make.bat ├── pages │ ├── funding.rst │ ├── getting_started.rst │ ├── install.rst │ ├── matlab_doc │ │ ├── data_loaders │ │ │ ├── load_conte69.rst │ │ │ ├── load_group_fc.rst │ │ │ ├── load_group_mpc.rst │ │ │ ├── load_mask.rst │ │ │ ├── load_metric.rst │ │ │ ├── load_parcellation.rst │ │ │ └── load_template.rst │ │ ├── examples │ │ │ ├── example_figs │ │ │ │ ├── colorscatter.png │ │ │ │ ├── colorsurface.png │ │ │ │ ├── connectivity_matrices.png │ │ │ │ ├── connectivity_matrix_schaefer_100.png │ │ │ │ ├── connectivity_matrix_schaefer_400.png │ │ │ │ ├── g1-2_schaefer_400_v2.png │ │ │ │ ├── g1_main_holdout_joint_v2.png │ │ │ │ ├── g1_main_holdout_noalign_v2.png │ │ │ │ ├── g1_main_holdout_procrustes_v2.png │ │ │ │ ├── g1_schaefer_400_approach_v2.png │ │ │ │ ├── g1_schaefer_400_kernel_v2.png │ │ │ │ ├── gettingstarted1.png │ │ │ │ ├── gettingstarted2.png │ │ │ │ ├── mpc_fc.png │ │ │ │ ├── msr_correlations.png │ │ │ │ ├── multimodal_gradients.png │ │ │ │ ├── schaefer_400.png │ │ │ │ ├── schaefer_400_G1G2.png │ │ │ │ ├── scree.png │ │ │ │ ├── t1wt2w_original.png │ │ │ │ └── t1wt2w_rotated.png │ │ │ ├── tutorial_1_gradient_creation.rst │ │ │ ├── tutorial_2_gradient_customization.rst │ │ │ └── tutorial_3_null_models.rst │ │ ├── index.rst │ │ ├── main_functionality │ │ │ ├── combine_surfaces.rst │ │ │ ├── compute_mem.rst │ │ │ ├── full2parcel.rst │ │ │ ├── gradientmaps.rst │ │ │ ├── moran_randomization.rst │ │ │ ├── parcel2full.rst │ │ │ ├── read_surface.rst │ │ │ ├── spin_permutations.rst │ │ │ ├── split_surfaces.rst │ │ │ ├── variogram.rst │ │ │ └── write_surface.rst │ │ ├── support_functions │ │ │ ├── SurfStatReadSurf1.rst │ │ │ ├── SurfStatWriteSurf1.rst │ │ │ ├── convert_surface.rst │ │ │ ├── diffusion_mapping.rst │ │ │ ├── labelmean.rst │ │ │ ├── laplacian_eigenmaps.rst │ │ │ ├── procrustes_alignment.rst │ │ │ └── surface_to_graph.rst │ │ └── visualization │ │ │ ├── gradient_in_euclidean.rst │ │ │ ├── plot_hemispheres.rst │ │ │ └── scree_plot.rst │ └── references.rst ├── python_doc │ ├── api_doc │ │ ├── brainspace.datasets.rst │ │ ├── brainspace.gradient.rst │ │ ├── brainspace.mesh.rst │ │ ├── brainspace.null_models.rst │ │ ├── brainspace.plotting.rst │ │ ├── brainspace.utils.rst │ │ ├── brainspace.vtk_interface.rst │ │ └── index_api.rst │ ├── auto_examples │ │ ├── auto_examples_jupyter.zip │ │ ├── auto_examples_python.zip │ │ ├── images │ │ │ ├── sphx_glr_plot_tutorial0_001.png │ │ │ ├── sphx_glr_plot_tutorial0_002.png │ │ │ ├── sphx_glr_plot_tutorial1_001.png │ │ │ ├── sphx_glr_plot_tutorial1_002.png │ │ │ ├── sphx_glr_plot_tutorial1_003.png │ │ │ ├── sphx_glr_plot_tutorial2_001.png │ │ │ ├── sphx_glr_plot_tutorial2_002.png │ │ │ ├── sphx_glr_plot_tutorial2_003.png │ │ │ ├── sphx_glr_plot_tutorial2_004.png │ │ │ ├── sphx_glr_plot_tutorial2_005.png │ │ │ ├── sphx_glr_plot_tutorial2_006.png │ │ │ ├── sphx_glr_plot_tutorial2_007.png │ │ │ ├── sphx_glr_plot_tutorial3_001.png │ │ │ ├── sphx_glr_plot_tutorial3_002.png │ │ │ ├── sphx_glr_plot_tutorial3_003.png │ │ │ ├── sphx_glr_plot_tutorial3_004.png │ │ │ ├── sphx_glr_plot_tutorial3_005.png │ │ │ └── thumb │ │ │ │ ├── sphx_glr_plot_tutorial0_thumb.png │ │ │ │ ├── sphx_glr_plot_tutorial1_thumb.png │ │ │ │ ├── sphx_glr_plot_tutorial2_thumb.png │ │ │ │ └── sphx_glr_plot_tutorial3_thumb.png │ │ ├── index.rst │ │ ├── plot_tutorial0.ipynb │ │ ├── plot_tutorial0.py │ │ ├── plot_tutorial0.py.md5 │ │ ├── plot_tutorial0.rst │ │ ├── plot_tutorial1.ipynb │ │ ├── plot_tutorial1.py │ │ ├── plot_tutorial1.py.md5 │ │ ├── plot_tutorial1.rst │ │ ├── plot_tutorial2.ipynb │ │ ├── plot_tutorial2.py │ │ ├── plot_tutorial2.py.md5 │ │ ├── plot_tutorial2.rst │ │ ├── plot_tutorial3.ipynb │ │ ├── plot_tutorial3.py │ │ ├── plot_tutorial3.py.md5 │ │ ├── plot_tutorial3.rst │ │ └── sg_execution_times.rst │ ├── index_intro.rst │ ├── index_python.rst │ └── vtk_wrap.rst └── requirements.txt ├── matlab ├── @GradientMaps │ ├── GradientMaps.m │ └── fit.m ├── analysis_code │ ├── @variogram │ │ └── variogram.m │ ├── compute_mem.m │ ├── diffusion_mapping.m │ ├── graph_is_connected.m │ ├── labelmean.m │ ├── laplacian_eigenmaps.m │ ├── moran_randomization.m │ ├── procrustes_alignment.m │ └── spin_permutations.m ├── datasets │ ├── data │ │ ├── .gitignore │ │ ├── fusion_tutorial │ │ │ └── vosdewael_200_mpc_matrix.csv │ │ ├── holdout_group │ │ │ ├── schaefer_100_mean_connectivity_matrix.csv │ │ │ ├── schaefer_200_mean_connectivity_matrix.csv │ │ │ ├── schaefer_300_mean_connectivity_matrix.csv │ │ │ ├── schaefer_400_mean_connectivity_matrix.csv │ │ │ ├── vosdewael_100_mean_connectivity_matrix.csv │ │ │ ├── vosdewael_200_mean_connectivity_matrix.csv │ │ │ ├── vosdewael_300_mean_connectivity_matrix.csv │ │ │ └── vosdewael_400_mean_connectivity_matrix.csv │ │ └── main_group │ │ │ ├── conte69_32k_curvature.csv │ │ │ ├── conte69_32k_t1wt2w.csv │ │ │ ├── conte69_32k_thickness.csv │ │ │ ├── schaefer_100_mean_connectivity_matrix.csv │ │ │ ├── schaefer_200_mean_connectivity_matrix.csv │ │ │ ├── schaefer_300_mean_connectivity_matrix.csv │ │ │ ├── schaefer_400_mean_connectivity_matrix.csv │ │ │ ├── vosdewael_100_mean_connectivity_matrix.csv │ │ │ ├── vosdewael_200_mean_connectivity_matrix.csv │ │ │ ├── vosdewael_300_mean_connectivity_matrix.csv │ │ │ └── vosdewael_400_mean_connectivity_matrix.csv │ ├── parcellations │ │ ├── mesulam_conte69.csv │ │ ├── schaefer_100_conte69.csv │ │ ├── schaefer_200_conte69.csv │ │ ├── schaefer_300_conte69.csv │ │ ├── schaefer_400_conte69.csv │ │ ├── vosdewael_100_conte69.csv │ │ ├── vosdewael_200_conte69.csv │ │ ├── vosdewael_300_conte69.csv │ │ └── vosdewael_400_conte69.csv │ ├── surfaces │ │ ├── conte69_32k_left_hemisphere.gii │ │ ├── conte69_32k_left_sphere.gii │ │ ├── conte69_32k_lh_midline_mask.csv │ │ ├── conte69_32k_lh_temporal_mask.csv │ │ ├── conte69_32k_rh_mask.csv │ │ ├── conte69_32k_rh_midline_mask.csv │ │ ├── conte69_32k_rh_temporal_mask.csv │ │ ├── conte69_32k_right_hemisphere.gii │ │ ├── conte69_32k_right_sphere.gii │ │ ├── conte69_32k_temporal_mask.csv │ │ ├── conte69_5k_left_hemisphere.gii │ │ ├── conte69_5k_midline_mask.csv │ │ ├── conte69_5k_right_hemisphere.gii │ │ ├── conte69_5k_vertex_indices.csv │ │ ├── fsa5.pial.lh.gii │ │ └── fsa5.pial.rh.gii │ └── template_gradients │ │ ├── conte69_32k_fc_gradient1.csv │ │ ├── conte69_32k_fc_gradient2.csv │ │ ├── conte69_32k_mpc_gradient1.csv │ │ └── conte69_32k_mpc_gradient2.csv ├── example_data_loaders │ ├── load_conte69.m │ ├── load_gradient.m │ ├── load_group_fc.m │ ├── load_group_mpc.m │ ├── load_marker.m │ ├── load_mask.m │ └── load_parcellation.m ├── plot_data │ ├── @plot_hemispheres │ │ ├── colorlimits.m │ │ ├── colormaps.m │ │ ├── labels.m │ │ ├── plot_hemispheres.m │ │ └── private 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