├── .codecov.yml ├── .codespellrc ├── .coveragerc ├── .gitattributes ├── .github ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE.md ├── ISSUE_TEMPLATE │ ├── 1_bug_report.yml │ ├── 2_feature_request.yml │ ├── 3_performance_impact_report.yml │ ├── 4_design_impact_report.yml │ ├── 5_infrastructure_impact_report.yml │ ├── 6_data_addition_request.yml │ ├── 7_documentation_impact_report.yml │ ├── 8_coverage_impact_report.yml │ ├── 9_coding_style_inconsistency_report.yml │ └── config.yml ├── dependabot.yml ├── labeler.yml └── workflows │ ├── benchmark.yml │ ├── build_docs.yml │ ├── check_format.yml │ ├── first_interaction.yml │ ├── label-pr.yml │ ├── nightly.yml │ ├── test.yml │ ├── test_template.yml │ └── test_viz.yml ├── .gitignore ├── .mailmap ├── .pre-commit-config.yaml ├── .spin └── cmds.py ├── AUTHOR ├── Changelog ├── LICENSE ├── Makefile ├── README.rst ├── bench.ini ├── benchmarks ├── README.rst ├── asv.conf.json ├── asv_compare.conf.json.tpl ├── asv_pip_nopep517.py └── benchmarks │ ├── __init__.py │ ├── bench_reconst.py │ ├── bench_segment.py │ └── bench_tracking.py ├── dipy ├── __init__.py ├── align │ ├── __init__.py │ ├── _public.py │ ├── bundlemin.pyx │ ├── cpd.py │ ├── crosscorr.pyx │ ├── expectmax.pyx │ ├── fused_types.pxd │ ├── imaffine.py │ ├── imwarp.py │ ├── meson.build │ ├── metrics.py │ ├── parzenhist.pyx │ ├── reslice.py │ ├── scalespace.py │ ├── streamlinear.py │ ├── streamwarp.py │ ├── sumsqdiff.pyx │ ├── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_api.py │ │ ├── test_crosscorr.py │ │ ├── test_expectmax.py │ │ ├── test_imaffine.py │ │ ├── test_imwarp.py │ │ ├── test_metrics.py │ │ ├── test_parzenhist.py │ │ ├── test_reslice.py │ │ ├── test_scalespace.py │ │ ├── test_streamlinear.py │ │ ├── test_streamwarp.py │ │ ├── test_sumsqdiff.py │ │ ├── test_transforms.py │ │ ├── test_vector_fields.py │ │ └── test_whole_brain_slr.py │ ├── transforms.pxd │ ├── transforms.pyx │ ├── vector_fields.pxd │ └── vector_fields.pyx ├── conftest.py ├── core │ ├── __init__.py │ ├── geometry.py │ ├── gradients.py │ ├── graph.py │ ├── histeq.py │ ├── interpolation.pxd │ ├── interpolation.pyx │ ├── math.pxd │ ├── math.pyx │ ├── meson.build │ ├── ndindex.py │ ├── onetime.py │ ├── optimize.py │ ├── profile.py │ ├── pyalloc.pxd │ ├── rng.py │ ├── sphere.py │ ├── sphere_stats.py │ ├── subdivide_octahedron.py │ ├── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_geometry.py │ │ ├── test_gradients.py │ │ ├── test_graph.py │ │ ├── test_interpolation.py │ │ ├── test_math.pyx │ │ ├── test_ndindex.py │ │ ├── test_optimize.py │ │ ├── test_rng.py │ │ ├── test_sphere.py │ │ └── test_subdivide_octahedron.py │ └── wavelet.py ├── data │ ├── 3shells-1000-2000-3500-N193.bval │ ├── 3shells-1000-2000-3500-N193.bvec │ ├── __init__.py │ ├── fetcher.py │ ├── files │ │ ├── 55dir_grad.bval │ │ ├── 55dir_grad.bvec │ │ ├── C.npy │ │ ├── C1.pkl.gz │ │ ├── C3.pkl.gz │ │ ├── EuDX_small_25.trk │ │ ├── S0_10slices.nii.gz │ │ ├── ScannerVectors_GQI101.txt │ │ ├── aniso_vox.nii.gz │ │ ├── ascm_out_test.nii.gz │ │ ├── cb_2.npz │ │ ├── circle.npy │ │ ├── dipy_colormaps.json │ │ ├── dki_constraint.npz │ │ ├── dki_constraint_0.npz │ │ ├── dki_constraint_2.npz │ │ ├── dki_constraint_4.npz │ │ ├── dki_constraint_SC.npz │ │ ├── dsi4169_b_table.txt │ │ ├── dsi515_b_table.txt │ │ ├── eg_3voxels.pkl │ │ ├── evenly_distributed_sphere_362.npz │ │ ├── evenly_distributed_sphere_642.npz │ │ ├── evenly_distributed_sphere_724.npz │ │ ├── fib0.pkl.gz │ │ ├── fib1.pkl.gz │ │ ├── fib2.pkl.gz │ │ ├── func_coef.nii.gz │ │ ├── func_discrete.nii.gz │ │ ├── grad_514.txt │ │ ├── gtab_3shell.txt │ │ ├── gtab_isbi2013_2shell.txt │ │ ├── gtab_taiwan_dsi.txt │ │ ├── hermite_constraint_0.npz │ │ ├── hermite_constraint_10.npz │ │ ├── hermite_constraint_2.npz │ │ ├── hermite_constraint_4.npz │ │ ├── hermite_constraint_6.npz │ │ ├── hermite_constraint_8.npz │ │ ├── life_matlab_rmse.npy │ │ ├── life_matlab_weights.npy │ │ ├── meson.build │ │ ├── minimal_bundles.zip │ │ ├── record_horizon.log.gz │ │ ├── repulsion100.npz │ │ ├── repulsion200.npz │ │ ├── repulsion724.npz │ │ ├── small_101D.bval │ │ ├── small_101D.bvec │ │ ├── small_101D.nii.gz │ │ ├── small_25.bval │ │ ├── small_25.bvec │ │ ├── small_25.nii.gz │ │ ├── small_64D.bval │ │ ├── small_64D.bvals.npy │ │ ├── small_64D.bvec │ │ ├── small_64D.gradients.npy │ │ ├── small_64D.nii │ │ ├── sphere_grad.txt │ │ ├── t1_coronal_slice.npy │ │ ├── tdesign45.txt │ │ ├── test_piesno.nii.gz │ │ ├── test_ui_text_block.npz │ │ └── tracks300.trk │ ├── meson.build │ └── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_data.py │ │ └── test_fetcher.py ├── denoise │ ├── __init__.py │ ├── adaptive_soft_matching.py │ ├── denspeed.pyx │ ├── enhancement_kernel.pyx │ ├── gibbs.py │ ├── localpca.py │ ├── meson.build │ ├── nlmeans.py │ ├── noise_estimate.py │ ├── patch2self.py │ ├── pca_noise_estimate.pyx │ ├── shift_twist_convolution.pyx │ └── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_ascm.py │ │ ├── test_denoise.py │ │ ├── test_gibbs.py │ │ ├── test_kernel.py │ │ ├── test_lpca.py │ │ ├── test_nlmeans.py │ │ ├── test_noise_estimate.py │ │ └── test_patch2self.py ├── direction │ ├── __init__.py │ ├── bootstrap_direction_getter.pyx │ ├── closest_peak_direction_getter.pxd │ ├── closest_peak_direction_getter.pyx │ ├── meson.build │ ├── peaks.py │ ├── pmf.pxd │ ├── pmf.pyx │ ├── probabilistic_direction_getter.pxd │ ├── probabilistic_direction_getter.pyx │ ├── ptt_direction_getter.pyx │ └── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_bootstrap_direction_getter.py │ │ ├── test_peaks.py │ │ ├── test_pmf.py │ │ ├── test_prob_direction_getter.py │ │ └── test_ptt_direction_getter.py ├── io │ ├── __init__.py │ ├── dpy.py │ ├── gradients.py │ ├── image.py │ ├── meson.build │ ├── peaks.py │ ├── pickles.py │ ├── stateful_surface.py │ ├── stateful_tractogram.py │ ├── streamline.py │ ├── surface.py │ ├── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_dpy.py │ │ ├── test_io.py │ │ ├── test_io_gradients.py │ │ ├── test_io_peaks.py │ │ ├── test_stateful_surface.py │ │ ├── test_stateful_tractogram.py │ │ ├── test_streamline.py │ │ ├── test_surface.py │ │ └── test_utils.py │ ├── utils.py │ └── vtk.py ├── meson.build ├── nn │ ├── __init__.py │ ├── meson.build │ ├── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_cnn_1denoiser.py │ │ ├── test_deepn4.py │ │ ├── test_evac.py │ │ ├── test_histo_resdnn.py │ │ ├── test_synb0.py │ │ ├── test_tf.py │ │ └── test_utils.py │ ├── tf │ │ ├── __init__.py │ │ ├── cnn_1d_denoising.py │ │ ├── deepn4.py │ │ ├── evac.py │ │ ├── histo_resdnn.py │ │ ├── meson.build │ │ ├── model.py │ │ └── synb0.py │ ├── torch │ │ ├── __init__.py │ │ ├── deepn4.py │ │ ├── evac.py │ │ ├── histo_resdnn.py │ │ └── meson.build │ └── utils.py ├── py.typed ├── reconst │ ├── __init__.py │ ├── base.py │ ├── bingham.py │ ├── cache.py │ ├── cross_validation.py │ ├── csdeconv.py │ ├── cti.py │ ├── dirspeed.pyx │ ├── dki.py │ ├── dki_micro.py │ ├── dsi.py │ ├── dti.py │ ├── eudx_direction_getter.pyx │ ├── forecast.py │ ├── fwdti.py │ ├── gqi.py │ ├── ivim.py │ ├── mapmri.py │ ├── mcsd.py │ ├── meson.build │ ├── msdki.py │ ├── multi_voxel.py │ ├── odf.py │ ├── qtdmri.py │ ├── qti.py │ ├── quick_squash.pyx │ ├── recspeed.pxd │ ├── recspeed.pyx │ ├── rumba.py │ ├── sfm.py │ ├── shm.py │ ├── shore.py │ ├── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_bingham.py │ │ ├── test_cache.py │ │ ├── test_cross_validation.py │ │ ├── test_csdeconv.py │ │ ├── test_cti.py │ │ ├── test_dki.py │ │ ├── test_dki_micro.py │ │ ├── test_dsi.py │ │ ├── test_dsi_deconv.py │ │ ├── test_dsi_metrics.py │ │ ├── test_dti.py │ │ ├── test_eudx_dg.py │ │ ├── test_forecast.py │ │ ├── test_fwdti.py │ │ ├── test_gqi.py │ │ ├── test_ivim.py │ │ ├── test_mapmri.py │ │ ├── test_mcsd.py │ │ ├── test_msdki.py │ │ ├── test_multi_voxel.py │ │ ├── test_odf.py │ │ ├── test_peak_finding.py │ │ ├── test_qtdmri.py │ │ ├── test_qti.py │ │ ├── test_reco_utils.py │ │ ├── test_rumba.py │ │ ├── test_sfm.py │ │ ├── test_shm.py │ │ ├── test_shore.py │ │ ├── test_shore_metrics.py │ │ ├── test_shore_odf.py │ │ ├── test_utils.py │ │ ├── test_vec_val_vect.py │ │ └── test_weights_method.py │ ├── utils.py │ ├── vec_val_sum.pyx │ └── weights_method.py ├── segment │ ├── __init__.py │ ├── bundles.py │ ├── clustering.py │ ├── clustering_algorithms.pyx │ ├── clusteringspeed.pxd │ ├── clusteringspeed.pyx │ ├── cythonutils.pxd │ ├── cythonutils.pyx │ ├── featurespeed.pxd │ ├── featurespeed.pyx │ ├── fss.py │ ├── mask.py │ ├── meson.build │ ├── metric.py │ ├── metricspeed.pxd │ ├── metricspeed.pyx │ ├── mrf.pyx │ ├── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_adjustment.py │ │ ├── test_bundles.py │ │ ├── test_clustering.py │ │ ├── test_feature.py │ │ ├── test_fss.py │ │ ├── test_mask.py │ │ ├── test_metric.py │ │ ├── test_mrf.py │ │ ├── test_qbx.py │ │ ├── test_quickbundles.py │ │ ├── test_tissue.py │ │ └── test_utils.py │ ├── threshold.py │ ├── tissue.py │ └── utils.py ├── sims │ ├── __init__.py │ ├── meson.build │ ├── phantom.py │ ├── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_phantom.py │ │ └── test_voxel.py │ └── voxel.py ├── stats │ ├── __init__.py │ ├── analysis.py │ ├── meson.build │ ├── qc.py │ ├── resampling.py │ ├── sketching.py │ └── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_analysis.py │ │ ├── test_qc.py │ │ ├── test_resampling.py │ │ └── test_sketching.py ├── testing │ ├── __init__.py │ ├── decorators.py │ ├── memory.py │ ├── meson.build │ ├── spherepoints.py │ └── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_decorators.py │ │ ├── test_memory.py │ │ └── test_testing.py ├── tests │ ├── __init__.py │ ├── meson.build │ ├── scriptrunner.py │ └── test_scripts.py ├── tracking │ ├── __init__.py │ ├── _utils.py │ ├── direction_getter.pxd │ ├── direction_getter.pyx │ ├── distances.pyx │ ├── fbcmeasures.pyx │ ├── learning.py │ ├── life.py │ ├── local_tracking.py │ ├── localtrack.pyx │ ├── mesh.py │ ├── meson.build │ ├── metrics.py │ ├── propspeed.pxd │ ├── propspeed.pyx │ ├── stopping_criterion.pxd │ ├── stopping_criterion.pyx │ ├── streamline.py │ ├── streamlinespeed.pxd │ ├── streamlinespeed.pyx │ ├── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_distances.py │ │ ├── test_fbc.py │ │ ├── test_learning.py │ │ ├── test_life.py │ │ ├── test_mesh.py │ │ ├── test_metrics.py │ │ ├── test_propspeed.pyx │ │ ├── test_stopping_criterion.py │ │ ├── test_streamline.py │ │ ├── test_track_volumes.py │ │ ├── test_tracker.py │ │ ├── test_tracking.py │ │ ├── test_tractogen.pyx │ │ └── test_utils.py │ ├── tracker.py │ ├── tracker_parameters.pxd │ ├── tracker_parameters.pyx │ ├── tractogen.pxd │ ├── tractogen.pyx │ ├── utils.py │ └── vox2track.pyx ├── utils │ ├── __init__.py │ ├── arrfuncs.py │ ├── compatibility.py │ ├── convert.py │ ├── deprecator.py │ ├── fast_numpy.pxd │ ├── fast_numpy.pyx │ ├── logging.py │ ├── meson.build │ ├── multiproc.py │ ├── omp.pxd │ ├── omp.pyx │ ├── optpkg.py │ ├── parallel.py │ ├── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_arrfuncs.py │ │ ├── test_compatibility.py │ │ ├── test_convert.py │ │ ├── test_deprecator.py │ │ ├── test_fast_numpy.pyx │ │ ├── test_logging.py │ │ ├── test_multiproc.py │ │ ├── test_omp.py │ │ ├── test_optpkg.py │ │ ├── test_parallel.py │ │ ├── test_tractogram.py │ │ ├── test_tripwire.py │ │ └── test_volume.py │ ├── tractogram.py │ ├── tripwire.py │ └── volume.py ├── viz │ ├── __init__.py │ ├── gmem.py │ ├── horizon │ │ ├── __init__.py │ │ ├── app.py │ │ ├── meson.build │ │ ├── tab │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── cluster.py │ │ │ ├── meson.build │ │ │ ├── peak.py │ │ │ ├── roi.py │ │ │ ├── slice.py │ │ │ ├── surface.py │ │ │ └── tests │ │ │ │ ├── __init__.py │ │ │ │ ├── meson.build │ │ │ │ ├── test_base.py │ │ │ │ ├── test_peak.py │ │ │ │ ├── test_roi.py │ │ │ │ ├── test_slices.py │ │ │ │ └── test_surface.py │ │ ├── util.py │ │ └── visualizer │ │ │ ├── __init__.py │ │ │ ├── cluster.py │ │ │ ├── meson.build │ │ │ ├── peak.py │ │ │ ├── slice.py │ │ │ └── surface.py │ ├── meson.build │ ├── panel.py │ ├── plotting.py │ ├── projections.py │ ├── regtools.py │ ├── streamline.py │ └── tests │ │ ├── __init__.py │ │ ├── meson.build │ │ ├── test_apps.py │ │ ├── test_fury.py │ │ ├── test_regtools.py │ │ ├── test_streamline.py │ │ └── test_util.py └── workflows │ ├── __init__.py │ ├── align.py │ ├── base.py │ ├── cli.py │ ├── combined_workflow.py │ ├── denoise.py │ ├── docstring_parser.py │ ├── flow_runner.py │ ├── io.py │ ├── mask.py │ ├── meson.build │ ├── multi_io.py │ ├── nn.py │ ├── reconst.py │ ├── segment.py │ ├── stats.py │ ├── tests │ ├── __init__.py │ ├── meson.build │ ├── test_align.py │ ├── test_denoise.py │ ├── test_docstring_parser.py │ ├── test_iap.py │ ├── test_io.py │ ├── test_masking.py │ ├── test_nn.py │ ├── test_reconst.py │ ├── test_reconst_csa_csd.py │ ├── test_reconst_dki.py │ ├── test_reconst_dsi.py │ ├── test_reconst_dti.py │ ├── test_reconst_ivim.py │ ├── test_reconst_mapmri.py │ ├── test_segment.py │ ├── test_stats.py │ ├── test_tracking.py │ ├── test_utils.py │ ├── test_viz.py │ ├── test_workflow.py │ └── workflow_tests_utils.py │ ├── tracking.py │ ├── utils.py │ ├── viz.py │ └── workflow.py ├── doc ├── .gitignore ├── Makefile ├── README.md ├── _static │ ├── colorfa.png │ ├── css │ │ ├── common │ │ │ ├── override.css │ │ │ └── variables.css │ │ └── dipy.css │ ├── dipy-banner.png │ ├── dipy-ws-header.png │ ├── dipy_paper_logo.jpg │ ├── hbm2015_exhibitors.jpg │ ├── images │ │ ├── examples │ │ │ ├── fbc_illustration.png │ │ │ └── stochastic_process.jpg │ │ └── logos │ │ │ ├── dipy-favicon.png │ │ │ ├── dipy-logo.png │ │ │ └── dipy_full_logo.png │ ├── pretty_tracks.png │ ├── simplified_tractography.png │ ├── spitfire_0.png │ ├── spitfire_hoped.png │ ├── spitfire_x.png │ ├── spitfire_y.png │ ├── three_brains_golden_new_small.png │ └── version_switcher.json ├── _templates │ ├── documentation.html │ └── layout.html ├── api_changes.rst ├── cite.rst ├── conf.py ├── devel │ ├── benchmarking.rst │ ├── bibliography.rst │ ├── coding_style_guideline.rst │ ├── commit_codes.rst │ ├── gitwash │ │ ├── branch_dropdown.png │ │ ├── branch_list.png │ │ ├── branch_list_compare.png │ │ ├── collaborators.png │ │ ├── configure_git.rst │ │ ├── development_workflow.rst │ │ ├── dot2_dot3.rst │ │ ├── following_latest.rst │ │ ├── forking_button.png │ │ ├── forking_hell.rst │ │ ├── git_development.rst │ │ ├── git_install.rst │ │ ├── git_intro.rst │ │ ├── git_links.inc │ │ ├── git_links.txt │ │ ├── git_resources.rst │ │ ├── index.rst │ │ ├── known_projects.inc │ │ ├── links.inc │ │ ├── maintainer_workflow.rst │ │ ├── patching.rst │ │ ├── pull_button.png │ │ ├── set_up_fork.rst │ │ └── this_project.inc │ ├── index.rst │ ├── installation_from_source.rst │ ├── intro.rst │ ├── make_release.rst │ └── toolchain.rst ├── developers.rst ├── examples │ ├── .gitignore │ ├── README.md │ ├── _valid_examples.toml │ ├── affine_registration_3d.py │ ├── affine_registration_masks.py │ ├── afq_tract_profiles.py │ ├── brain_extraction_dwi.py │ ├── bundle_assignment_maps.py │ ├── bundle_extraction.py │ ├── bundle_group_registration.py │ ├── bundle_registration.py │ ├── bundle_shape_similarity.py │ ├── bundlewarp_registration.py │ ├── cluster_confidence.py │ ├── combined_workflow_creation.py │ ├── contextual_enhancement.py │ ├── denoise_ascm.py │ ├── denoise_gibbs.py │ ├── denoise_localpca.py │ ├── denoise_mppca.py │ ├── denoise_nlmeans.py │ ├── denoise_patch2self.py │ ├── fast_streamline_search.py │ ├── fiber_to_bundle_coherence.py │ ├── gradients_spheres.py │ ├── histology_resdnn.py │ ├── kfold_xval.py │ ├── linear_fascicle_evaluation.py │ ├── motion_correction.py │ ├── path_length_map.py │ ├── piesno.py │ ├── quick_start.py │ ├── reconst_bingham.py │ ├── reconst_csa.py │ ├── reconst_csa_parallel.py │ ├── reconst_csd.py │ ├── reconst_csd_parallel.py │ ├── reconst_cti.py │ ├── reconst_dki.py │ ├── reconst_dki_micro.py │ ├── reconst_dsi.py │ ├── reconst_dsi_metrics.py │ ├── reconst_dsid.py │ ├── reconst_dti.py │ ├── reconst_forecast.py │ ├── reconst_fwdti.py │ ├── reconst_gqi.py │ ├── reconst_ivim.py │ ├── reconst_mapmri.py │ ├── reconst_mcsd.py │ ├── reconst_msdki.py │ ├── reconst_qtdmri.py │ ├── reconst_qti.py │ ├── reconst_qtiplus.py │ ├── reconst_rumba.py │ ├── reconst_sfm.py │ ├── reconst_sh.py │ ├── reconst_shore.py │ ├── reconst_shore_metrics.py │ ├── register_binary_fuzzy.py │ ├── reslice_datasets.py │ ├── restore_dti.py │ ├── segment_clustering_features.py │ ├── segment_clustering_metrics.py │ ├── segment_extending_clustering_framework.py │ ├── segment_quickbundles.py │ ├── simulate_dki.py │ ├── simulate_multi_tensor.py │ ├── snr_in_cc.py │ ├── streamline_formats.py │ ├── streamline_length.py │ ├── streamline_registration.py │ ├── streamline_tools.py │ ├── surface_seed.py │ ├── syn_registration_2d.py │ ├── syn_registration_3d.py │ ├── tissue_classification.py │ ├── tissue_classification_dam.py │ ├── tracking_bootstrap_peaks.py │ ├── tracking_deterministic.py │ ├── tracking_disco_phantom.py │ ├── tracking_introduction_eudx.py │ ├── tracking_pft.py │ ├── tracking_probabilistic.py │ ├── tracking_ptt.py │ ├── tracking_rumba.py │ ├── tracking_sfm.py │ ├── tracking_stopping_criterion.py │ ├── viz_advanced.py │ ├── viz_bundles.py │ ├── viz_horizon.py │ ├── viz_roi_contour.py │ ├── viz_slice.py │ └── workflow_creation.py ├── examples_built │ ├── .gitignore │ └── README ├── faq.rst ├── gimbal_lock.rst ├── glossary.rst ├── index.rst ├── interfaces │ ├── basic_flow.rst │ ├── buan_flow.rst │ ├── bundle_segmentation_flow.rst │ ├── bundlewarp_registration_flow.rst │ ├── data_fetch.rst │ ├── denoise_flow.rst │ ├── gibbs_unringing_flow.rst │ ├── index.rst │ ├── motion_flow.rst │ ├── reconstruction_flow.rst │ ├── registration_flow.rst │ ├── tracking_flow.rst │ └── viz_flow.rst ├── links_names.inc ├── make.bat ├── old_highlights.rst ├── old_news.rst ├── recipes.rst ├── reconstruction_models_list.rst ├── references.bib ├── release_notes │ ├── release0.10.rst │ ├── release0.11.rst │ ├── release0.12.rst │ ├── release0.13.rst │ ├── release0.14.rst │ ├── release0.15.rst │ ├── release0.16.rst │ ├── release0.6.rst │ ├── release0.7.rst │ ├── release0.8.rst │ ├── release0.9.rst │ ├── release1.0.rst │ ├── release1.1.rst │ ├── release1.10.rst │ ├── release1.11.rst │ ├── release1.2.rst │ ├── release1.3.rst │ ├── release1.4.1.rst │ ├── release1.4.rst │ ├── release1.5.rst │ ├── release1.6.rst │ ├── release1.7.rst │ ├── release1.8.rst │ └── release1.9.rst ├── sphinxext │ ├── docimage_scrap.py │ ├── github.py │ ├── math_dollar.py │ └── prepare_gallery.py ├── stateoftheart.rst ├── subscribe.rst ├── theory │ ├── b_and_q.rst │ ├── bmatrix.rst │ ├── gqi.rst │ ├── index.rst │ ├── sh_basis.rst │ ├── spherical.rst │ ├── spherical_coordinates.png │ └── spherical_coordinates.svg ├── tools │ ├── LICENSE.txt │ ├── apigen.py │ ├── build_modref_templates.py │ └── docgen_cmd.py ├── tractography_methods_list.rst ├── upload-gh-pages.sh ├── upload_docs.py └── user_guide │ ├── bibliography.rst │ ├── data.rst │ ├── dataset_list.rst │ ├── dependencies.rst │ ├── getting_started.rst │ ├── index.rst │ ├── installation.rst │ ├── introduction.rst │ └── mission.rst ├── meson.build ├── pyproject.toml ├── requirements.txt ├── requirements ├── all.txt ├── benchmark.txt ├── build.txt ├── default.txt ├── dev.txt ├── doc.txt ├── ml.txt ├── optional.txt ├── style.txt ├── test.txt └── viz.txt ├── ruff.toml ├── src ├── conditional_omp.h ├── ctime.pxd ├── cythonutils.h ├── dpy_math.h └── safe_openmp.pxd └── tools ├── build_dmgs.py ├── build_release ├── ci ├── activate_env.sh ├── archives │ ├── .travis.yml.old │ ├── appveyor.yml │ ├── azure-pipelines.yml.old │ ├── create_env_install_dependencies.sh │ ├── linux.yml │ ├── osx.yml │ └── windows.yml ├── deploy_doc.sh ├── install.ps1 ├── install.sh ├── 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