├── .coveragerc ├── .devcontainer ├── Dockerfile ├── devcontainer.json └── setup_container.sh ├── .dvc ├── .gitignore ├── config └── test_descriptors.yml ├── .dvcignore ├── .gitattributes ├── .github └── workflows │ ├── freeze_requirements.yml │ ├── publish_to_testpypi.yml │ ├── test-ml.yml │ ├── test.yml │ └── test_tutorials.yml ├── .gitignore ├── .pep8speaks.yml ├── .python-version ├── .readthedocs.yaml ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── cibuildwheel.toml ├── codecov.yml ├── conftest.py ├── docs ├── Makefile ├── make.bat ├── pull_request_template.md ├── requirements.txt └── source │ ├── _static │ ├── bash │ │ ├── bundle_analysis │ │ │ ├── bundle_diameter_fitting_function.sh │ │ │ ├── create_population_template.sh │ │ │ └── profilometry.sh │ │ ├── connectivity │ │ │ └── connectivity.sh │ │ ├── reconst │ │ │ ├── aodf_scripts.sh │ │ │ ├── btensor_scripts.sh │ │ │ ├── msmt_fodf.sh │ │ │ ├── mti_scripts.sh │ │ │ ├── qball_metrics.sh │ │ │ └── ssst_fodf.sh │ │ └── tractogram_manipulation │ │ │ ├── streamlines_math.sh │ │ │ └── tractogram_math.sh │ ├── images │ │ ├── b0_mean.png │ │ ├── eudx_tractogram.png │ │ ├── fa.png │ │ ├── prob_tractogram.png │ │ ├── rgb.png │ │ ├── scil_MTR.gif │ │ ├── scil_MTsat.gif │ │ ├── scil_ihMTR.gif │ │ ├── scil_ihMTsat.gif │ │ ├── scil_ihmt_explanation.png │ │ ├── scil_screenshot_volume_mosaic_overlap_t1.png │ │ ├── scil_screenshot_volume_mosaic_overlap_t1_matrix_cmap.png │ │ ├── scil_screenshot_volume_mosaic_overlap_t1_tisue_map.png │ │ ├── scil_screenshot_volume_mosaic_overlap_tissue_map.png │ │ ├── scilpy_paper_figure1.png │ │ ├── scilpy_paper_figure2.png │ │ ├── scilpy_paper_figure3.png │ │ ├── scilpy_paper_figure4.png │ │ ├── scilpy_paper_figure5.png │ │ ├── tractogram_math_intersection.png │ │ ├── tractogram_math_tutorial_data.png │ │ └── tractogram_math_upsampling.png │ └── my_style.css │ ├── conf.py │ ├── documentation │ ├── bundle_analysis │ │ ├── create_population_template.rst │ │ ├── index.rst │ │ ├── profilometry.rst │ │ ├── tractogram_segmentation.rst │ │ └── tractometry.rst │ ├── connectivity │ │ ├── connectivity.rst │ │ └── index.rst │ ├── getting_started.rst │ ├── reconstruction │ │ ├── aodf_scripts.rst │ │ ├── btensor_scripts.rst │ │ ├── index.rst │ │ ├── msmt_fodf.rst │ │ ├── mti_scripts.rst │ │ ├── qball_metrics.rst │ │ └── ssst_fodf.rst │ ├── scilpy_paper_index.rst │ ├── start_to_finish_pipelines │ │ ├── from_raw_data_to_tractogram.rst │ │ ├── index.rst │ │ ├── using_bash.rst │ │ └── using_nextflow.rst │ ├── tracking │ │ ├── dev_tracking.rst │ │ ├── fibertube_tracking.rst │ │ ├── index.rst │ │ └── local_tracking.rst │ ├── tractogram_manipulation │ │ ├── index.rst │ │ ├── streamlines_math.rst │ │ ├── tractogram_math.rst │ │ ├── tractogram_registration.rst │ │ └── using_trk_or_tck.rst │ ├── utils │ │ ├── construct_participants_tsv_file.rst │ │ ├── devcontainer.rst │ │ └── index.rst │ ├── visualization │ │ ├── colors.rst │ │ ├── create_overlapping_slice_mosaics.rst │ │ └── index.rst │ └── volumes_manip │ │ ├── cropping.rst │ │ └── index.rst │ ├── fake_files │ ├── streamlines_metrics.py │ └── voxel_boundary_intersection.py │ ├── index.rst │ └── modules │ ├── scilpy.connectivity.rst │ ├── scilpy.denoise.rst │ ├── scilpy.dwi.rst │ ├── scilpy.gpuparallel.rst │ ├── scilpy.gradients.rst │ ├── scilpy.image.rst │ ├── scilpy.io.rst │ ├── scilpy.maths.rst │ ├── scilpy.ml.rst │ ├── scilpy.preprocessing.rst │ ├── scilpy.reconst.rst │ ├── scilpy.rst │ ├── scilpy.segment.rst │ ├── scilpy.stats.rst │ ├── scilpy.surfaces.rst │ ├── scilpy.tracking.rst │ ├── scilpy.tractanalysis.rst │ ├── scilpy.tractograms.rst │ ├── scilpy.utils.rst │ └── scilpy.viz.rst ├── pyproject.toml ├── pytest.ini ├── setup.py └── src └── scilpy ├── __init__.py ├── cli ├── __init__.py ├── scil_NODDI_maps.py ├── scil_NODDI_priors.py ├── scil_aodf_metrics.py ├── scil_bids_validate.py ├── scil_bingham_metrics.py ├── scil_btensor_metrics.py ├── scil_bundle_alter_to_target_dice.py ├── scil_bundle_clean_qbx_clusters.py ├── scil_bundle_compute_centroid.py ├── scil_bundle_compute_endpoints_map.py ├── scil_bundle_diameter.py ├── scil_bundle_explore_bundleseg.py ├── scil_bundle_filter_by_occurrence.py ├── scil_bundle_fixel_analysis.py ├── scil_bundle_generate_priors.py ├── scil_bundle_label_map.py ├── scil_bundle_mean_fixel_afd.py ├── scil_bundle_mean_fixel_afd_from_hdf5.py ├── scil_bundle_mean_fixel_bingham_metric.py ├── scil_bundle_mean_fixel_mrds_metric.py ├── scil_bundle_mean_std.py ├── scil_bundle_pairwise_comparison.py ├── scil_bundle_reject_outliers.py ├── scil_bundle_score_many_bundles_one_tractogram.py ├── scil_bundle_score_same_bundle_many_segmentations.py ├── scil_bundle_shape_measures.py ├── scil_bundle_uniformize_endpoints.py ├── scil_bundle_volume_per_label.py ├── scil_connectivity_compare_populations.py ├── scil_connectivity_compute_matrices.py ├── scil_connectivity_compute_pca.py ├── scil_connectivity_compute_simple_matrix.py ├── scil_connectivity_filter.py ├── scil_connectivity_functional_graph_measures.py ├── scil_connectivity_hdf5_average_density_map.py ├── scil_connectivity_math.py ├── scil_connectivity_normalize.py ├── scil_connectivity_pairwise_agreement.py ├── scil_connectivity_print_filenames.py ├── scil_connectivity_reorder_rois.py ├── scil_connectivity_structural_graph_measures.py ├── scil_data_download.py ├── scil_denoising_nlmeans.py ├── scil_dki_metrics.py ├── scil_dti_convert_tensors.py ├── scil_dti_metrics.py ├── scil_dwi_apply_bias_field.py ├── scil_dwi_compute_snr.py ├── scil_dwi_concatenate.py ├── scil_dwi_convert_FDF.py ├── scil_dwi_detect_volume_outliers.py ├── scil_dwi_extract_b0.py ├── scil_dwi_extract_shell.py ├── scil_dwi_powder_average.py ├── scil_dwi_prepare_eddy_command.py ├── scil_dwi_prepare_topup_command.py ├── scil_dwi_reorder_philips.py ├── scil_dwi_split_by_indices.py ├── scil_dwi_to_sh.py ├── scil_fibertube_compute_density.py ├── scil_fibertube_score_tractogram.py ├── scil_fibertube_tracking.py ├── scil_fodf_bundleparc.py ├── scil_fodf_max_in_ventricles.py ├── scil_fodf_memsmt.py ├── scil_fodf_metrics.py ├── scil_fodf_msmt.py ├── scil_fodf_ssst.py ├── scil_fodf_to_bingham.py ├── scil_freewater_maps.py ├── scil_freewater_priors.py ├── scil_frf_mean.py ├── scil_frf_memsmt.py ├── scil_frf_msmt.py ├── scil_frf_set_diffusivities.py ├── scil_frf_ssst.py ├── scil_get_version.py ├── scil_gradients_apply_transform.py ├── scil_gradients_convert.py ├── scil_gradients_generate_sampling.py ├── scil_gradients_modify_axes.py ├── scil_gradients_normalize_bvecs.py ├── scil_gradients_round_bvals.py ├── scil_gradients_validate_correct.py ├── scil_gradients_validate_correct_eddy.py ├── scil_gradients_validate_sampling.py ├── scil_header_print_info.py ├── scil_header_validate_compatibility.py ├── scil_json_convert_entries_to_xlsx.py ├── scil_json_harmonize_entries.py ├── scil_json_merge_entries.py ├── scil_labels_combine.py ├── scil_labels_dilate.py ├── scil_labels_from_mask.py ├── scil_labels_remove.py ├── scil_labels_split_volume_by_ids.py ├── scil_labels_split_volume_from_lut.py ├── scil_lesions_generate_nawm.py ├── scil_lesions_harmonize_labels.py ├── scil_lesions_info.py ├── scil_mrds_metrics.py ├── scil_mrds_select_number_of_tensors.py ├── scil_mti_adjust_B1_header.py ├── scil_mti_maps_MT.py ├── scil_mti_maps_ihMT.py ├── scil_plot_stats_per_point.py ├── scil_qball_metrics.py ├── scil_rgb_convert.py ├── scil_search_keywords.py ├── scil_sh_convert.py ├── scil_sh_fusion.py ├── scil_sh_to_aodf.py ├── scil_sh_to_rish.py ├── scil_sh_to_sf.py ├── scil_stats_group_comparison.py ├── scil_surface_apply_transform.py ├── scil_surface_convert.py ├── scil_surface_create.py ├── scil_surface_flip.py ├── scil_surface_smooth.py ├── scil_tracking_local.py ├── scil_tracking_local_dev.py ├── scil_tracking_pft.py ├── scil_tracking_pft_maps.py ├── scil_tracking_pft_maps_edit.py ├── scil_tractogram_apply_transform.py ├── scil_tractogram_apply_transform_to_hdf5.py ├── scil_tractogram_assign_custom_color.py ├── scil_tractogram_assign_uniform_color.py ├── scil_tractogram_commit.py ├── scil_tractogram_compress.py ├── scil_tractogram_compute_TODI.py ├── scil_tractogram_compute_density_map.py ├── scil_tractogram_convert.py ├── scil_tractogram_convert_hdf5_to_trk.py ├── scil_tractogram_convert_trk_to_hdf5.py ├── scil_tractogram_count_streamlines.py ├── scil_tractogram_cut_streamlines.py ├── scil_tractogram_detect_loops.py ├── scil_tractogram_dpp_math.py ├── scil_tractogram_dps_math.py ├── scil_tractogram_extract_ushape.py ├── scil_tractogram_filter_by_anatomy.py ├── scil_tractogram_filter_by_length.py ├── scil_tractogram_filter_by_orientation.py ├── scil_tractogram_filter_by_roi.py ├── scil_tractogram_filter_collisions.py ├── scil_tractogram_flip.py ├── scil_tractogram_math.py ├── scil_tractogram_pairwise_comparison.py ├── scil_tractogram_print_info.py ├── scil_tractogram_project_map_to_streamlines.py ├── scil_tractogram_project_streamlines_to_map.py ├── scil_tractogram_qbx.py ├── scil_tractogram_register.py ├── scil_tractogram_remove_invalid.py ├── scil_tractogram_resample.py ├── scil_tractogram_resample_nb_points.py ├── scil_tractogram_seed_density_map.py ├── scil_tractogram_segment_connections_from_labels.py ├── scil_tractogram_segment_with_ROI_and_score.py ├── scil_tractogram_segment_with_bundleseg.py ├── scil_tractogram_segment_with_recobundles.py ├── scil_tractogram_shuffle.py ├── scil_tractogram_smooth.py ├── scil_tractogram_split.py ├── scil_viz_bingham_fit.py ├── scil_viz_bundle.py ├── scil_viz_bundle_screenshot_mni.py ├── scil_viz_bundle_screenshot_mosaic.py ├── scil_viz_connectivity.py ├── scil_viz_dti_screenshot.py ├── scil_viz_fodf.py ├── scil_viz_gradients_screenshot.py ├── scil_viz_tractogram_collisions.py ├── scil_viz_tractogram_seeds.py ├── scil_viz_tractogram_seeds_3d.py ├── scil_viz_volume_histogram.py ├── scil_viz_volume_scatterplot.py ├── scil_viz_volume_screenshot.py ├── scil_viz_volume_screenshot_mosaic.py ├── scil_volume_apply_transform.py ├── scil_volume_b0_synthesis.py ├── scil_volume_count_non_zero_voxels.py ├── scil_volume_crop.py ├── scil_volume_distance_map.py ├── scil_volume_flip.py ├── scil_volume_math.py ├── scil_volume_pairwise_comparison.py ├── scil_volume_remove_outliers_ransac.py ├── scil_volume_resample.py ├── scil_volume_reshape.py ├── scil_volume_reslice_to_reference.py ├── scil_volume_stats_in_ROI.py ├── scil_volume_stats_in_labels.py ├── scil_volume_validate_correct_strides.py └── tests │ ├── __init__.py │ ├── test_NODDI_maps.py │ ├── test_NODDI_priors.py │ ├── test_aodf_metrics.py │ ├── test_bids_validate.py │ ├── test_bingham_metrics.py │ ├── test_btensor_metrics.py │ ├── test_bundle_alter_to_target_dice.py │ ├── test_bundle_clean_qbx_clusters.py │ ├── test_bundle_compute_centroid.py │ ├── test_bundle_compute_endpoints_map.py │ ├── test_bundle_diameter.py │ ├── test_bundle_explore_bundleseg.py │ ├── test_bundle_filter_by_occurrence.py │ ├── test_bundle_fixel_analysis.py │ ├── test_bundle_generate_priors.py │ ├── test_bundle_label_map.py │ ├── test_bundle_mean_fixel_afd.py │ ├── test_bundle_mean_fixel_afd_from_hdf5.py │ ├── test_bundle_mean_fixel_bingham_metric.py │ ├── test_bundle_mean_fixel_mrds_metric.py │ ├── test_bundle_mean_std.py │ ├── test_bundle_pairwise_comparison.py │ ├── test_bundle_reject_outliers.py │ ├── test_bundle_score_many_bundles_one_tractogram.py │ ├── test_bundle_score_same_bundle_many_segmentations.py │ ├── test_bundle_shape_measures.py │ ├── test_bundle_uniformize_endpoints.py │ ├── test_bundle_volume_per_label.py │ ├── test_connectivity_compare_populations.py │ ├── test_connectivity_compute_matrices.py │ ├── test_connectivity_compute_pca.py │ ├── test_connectivity_compute_simple_matrix.py │ ├── test_connectivity_filter.py │ ├── test_connectivity_functional_graph_measures.py │ ├── test_connectivity_hdf5_average_density_map.py │ ├── test_connectivity_math.py │ ├── test_connectivity_normalize.py │ ├── test_connectivity_pairwise_agreement.py │ ├── test_connectivity_print_filenames.py │ ├── test_connectivity_reorder_rois.py │ ├── test_connectivity_structural_graph_measures.py │ ├── test_data_download.py │ ├── test_denoising_nlmeans.py │ ├── test_dki_metrics.py │ ├── test_dti_convert_tensors.py │ ├── test_dti_metrics.py │ ├── test_dwi_apply_bias_field.py │ ├── test_dwi_compute_snr.py │ ├── test_dwi_concatenate.py │ ├── test_dwi_convert_FDF.py │ ├── test_dwi_detect_volume_outliers.py │ ├── test_dwi_extract_b0.py │ ├── test_dwi_extract_shell.py │ ├── test_dwi_powder_average.py │ ├── test_dwi_prepare_eddy_command.py │ ├── test_dwi_prepare_topup_command.py │ ├── test_dwi_reorder_philips.py │ ├── test_dwi_split_by_indices.py │ ├── test_dwi_to_sh.py │ ├── test_fibertube_compute_density.py │ ├── test_fibertube_score_tractogram.py │ ├── test_fibertube_tracking.py │ ├── test_fodf_bundleparc.py │ ├── test_fodf_max_in_ventricles.py │ ├── test_fodf_memsmt.py │ ├── test_fodf_metrics.py │ ├── test_fodf_msmt.py │ ├── test_fodf_ssst.py │ ├── test_fodf_to_bingham.py │ ├── test_freewater_maps.py │ ├── test_freewater_priors.py │ ├── test_frf_mean.py │ ├── test_frf_memsmt.py │ ├── test_frf_msmt.py │ ├── test_frf_set_diffusivities.py │ ├── test_frf_ssst.py │ ├── test_get_version.py │ ├── test_gradients_apply_transform.py │ ├── test_gradients_convert.py │ ├── test_gradients_generate_sampling.py │ ├── test_gradients_modify_axes.py │ ├── test_gradients_normalize_bvecs.py │ ├── test_gradients_round_bvals.py │ ├── test_gradients_validate_correct.py │ ├── test_gradients_validate_correct_eddy.py │ ├── test_gradients_validate_sampling.py │ ├── test_header_print_info.py │ ├── test_header_validate_compatibility.py │ ├── test_json_convert_entries_to_xlsx.py │ ├── test_json_harmonize_entries.py │ ├── test_json_merge_entries.py │ ├── test_labels_combine.py │ ├── test_labels_dilate.py │ ├── test_labels_from_mask.py │ ├── test_labels_remove.py │ ├── test_labels_split_volume_by_ids.py │ ├── test_labels_split_volume_from_lut.py │ ├── test_lesions_generate_nawm.py │ ├── test_lesions_harmonize_labels.py │ ├── test_lesions_info.py │ ├── test_mrds_metrics.py │ ├── test_mrds_select_number_of_tensors.py │ ├── test_mti_adjust_B1_header.py │ ├── test_mti_maps_MT.py │ ├── test_mti_maps_ihMT.py │ ├── test_plot_stats_per_point.py │ ├── test_qball_metrics.py │ ├── test_rgb_convert.py │ ├── test_search_keywords.py │ ├── test_sh_convert.py │ ├── test_sh_fusion.py │ ├── test_sh_to_aodf.py │ ├── test_sh_to_rish.py │ ├── test_sh_to_sf.py │ ├── test_stats_group_comparison.py │ ├── test_surface_apply_transform.py │ ├── test_surface_convert.py │ ├── test_surface_create.py │ ├── test_surface_flip.py │ ├── test_surface_smooth.py │ ├── test_tracking_local.py │ ├── test_tracking_local_dev.py │ ├── test_tracking_pft.py │ ├── test_tracking_pft_maps.py │ ├── test_tracking_pft_maps_edit.py │ ├── test_tractogram_apply_transform.py │ ├── test_tractogram_apply_transform_to_hdf5.py │ ├── test_tractogram_assign_custom_color.py │ ├── test_tractogram_assign_uniform_color.py │ ├── test_tractogram_commit.py │ ├── test_tractogram_compress.py │ ├── test_tractogram_compute_TODI.py │ ├── test_tractogram_compute_density_map.py │ ├── test_tractogram_convert.py │ ├── test_tractogram_convert_hdf5_to_trk.py │ ├── test_tractogram_convert_trk_to_hdf5.py │ ├── test_tractogram_count_streamlines.py │ ├── test_tractogram_cut_streamlines.py │ ├── test_tractogram_detect_loops.py │ ├── test_tractogram_dpp_math.py │ ├── test_tractogram_dps_math.py │ ├── test_tractogram_extract_ushape.py │ ├── test_tractogram_filter_by_anatomy.py │ ├── test_tractogram_filter_by_length.py │ ├── test_tractogram_filter_by_orientation.py │ ├── test_tractogram_filter_by_roi.py │ ├── test_tractogram_filter_collisions.py │ ├── test_tractogram_flip.py │ ├── test_tractogram_math.py │ ├── test_tractogram_pairwise_comparison.py │ ├── test_tractogram_print_info.py │ ├── test_tractogram_project_map_to_streamlines.py │ ├── test_tractogram_project_streamlines_to_map.py │ ├── test_tractogram_qbx.py │ ├── test_tractogram_register.py │ ├── test_tractogram_remove_invalid.py │ ├── test_tractogram_resample.py │ ├── test_tractogram_resample_nb_points.py │ ├── test_tractogram_seed_density_map.py │ ├── test_tractogram_segment_connections_from_labels.py │ ├── test_tractogram_segment_with_ROI_and_score.py │ ├── test_tractogram_segment_with_bundleseg.py │ ├── test_tractogram_segment_with_recobundles.py │ ├── test_tractogram_shuffle.py │ ├── test_tractogram_smooth.py │ ├── test_tractogram_split.py │ ├── test_viz_bingham_fit.py │ ├── test_viz_bundle.py │ ├── test_viz_bundle_screenshot_mni.py │ ├── test_viz_bundle_screenshot_mosaic.py │ ├── test_viz_connectivity.py │ ├── test_viz_dti_screenshot.py │ ├── test_viz_fodf.py │ ├── test_viz_gradients_screenshot.py │ ├── test_viz_tractogram_collisions.py │ ├── test_viz_tractogram_seeds.py │ ├── test_viz_tractogram_seeds_3d.py │ ├── test_viz_volume_histogram.py │ ├── test_viz_volume_scatterplot.py │ ├── test_viz_volume_screenshot.py │ ├── test_viz_volume_screenshot_mosaic.py │ ├── test_volume_apply_transform.py │ ├── test_volume_b0_synthesis.py │ ├── test_volume_count_non_zero_voxels.py │ ├── test_volume_crop.py │ ├── test_volume_distance_map.py │ ├── test_volume_flip.py │ ├── test_volume_math.py │ ├── test_volume_pairwise_comparison.py │ ├── test_volume_remove_outliers_ransac.py │ ├── test_volume_resample.py │ ├── test_volume_reshape.py │ ├── test_volume_reslice_to_reference.py │ ├── test_volume_stats_in_ROI.py │ ├── test_volume_stats_in_labels.py │ └── test_volume_validate_correct_strides.py ├── connectivity ├── __init__.py ├── connectivity.py ├── matrix_tools.py └── tests │ ├── test_connectivity.py │ └── test_matrix_tools.py ├── data ├── LUT │ ├── dk_aggregate_structures.json │ ├── freesurfer_desikan_killiany.json │ └── freesurfer_subcortical.json ├── __init__.py ├── mni_icbm152_t1_tal_nlin_asym_09c_masked_2_5.nii.gz └── vocabulary.json ├── denoise ├── __init__.py ├── aodf_filter.cl ├── asym_filtering.py └── tests │ └── test_asym_filtering.py ├── dwi ├── __init__.py ├── operations.py ├── tests │ ├── __init__.py │ ├── test_operations.py │ └── test_utils.py └── utils.py ├── gpuparallel ├── __init__.py └── opencl_utils.py ├── gradients ├── __init__.py ├── bvec_bval_tools.py ├── gen_gradient_sampling.py ├── optimize_gradient_sampling.py ├── tests │ ├── test_bvec_bval_tools.py │ ├── test_gen_gradient_sampling.py │ ├── test_gradients_utils.py │ └── test_optimize_gradient_sampling.py └── utils.py ├── image ├── __init__.py ├── labels.py ├── reslice.py ├── tests │ ├── __init__.py │ ├── test_labels.py │ ├── test_volume_math.py │ ├── test_volume_metrics.py │ └── test_volume_operations.py ├── utils.py ├── volume_b0_synthesis.py ├── volume_math.py ├── volume_metrics.py ├── volume_operations.py └── volume_space_management.py ├── io ├── __init__.py ├── btensor.py ├── deprecator.py ├── dvc.py ├── fetcher.py ├── gradients.py ├── hdf5.py ├── image.py ├── mti.py ├── streamlines.py ├── tensor.py ├── utils.py └── varian_fdf.py ├── maths ├── __init__.py └── utils.py ├── ml ├── __init__.py ├── bundleparc │ ├── __init__.py │ ├── attention.py │ ├── bundleparcnet.py │ ├── encodings.py │ ├── labels.py │ ├── predict.py │ ├── tests │ │ └── test_bundleparc_utils.py │ └── utils.py └── utils.py ├── preprocessing ├── __init__.py └── distortion_correction.py ├── reconst ├── __init__.py ├── aodf.py ├── bingham.py ├── divide.py ├── fiber_coherence.py ├── fodf.py ├── frf.py ├── mti.py ├── sh.py ├── tests │ ├── test_aodf.py │ ├── test_bingham.py │ ├── test_divide.py │ ├── test_fiber_coherence.py │ ├── test_fodf.py │ ├── test_frf.py │ ├── test_mti.py │ ├── test_sh.py │ └── test_utils.py └── utils.py ├── segment ├── __init__.py ├── bundleseg.py ├── streamlines.py ├── tests │ └── test_tractogram_from_roi.py ├── tractogram_from_roi.py └── voting_scheme.py ├── stats ├── __init__.py ├── matrix_stats.py ├── stats.py ├── tests │ └── test_matrix_stats.py └── utils.py ├── surfaces ├── __init__.py ├── surface_operations.py ├── tests │ ├── test_surface_operations.py │ └── test_surfaces_utils.py └── utils.py ├── tests ├── arrays.py ├── dict.py ├── streamlines.py └── utils.py ├── tracking ├── __init__.py ├── fibertube_utils.py ├── local_tracking.cl ├── propagator.py ├── rap.py ├── seed.py ├── tests │ ├── test_propagator.py │ ├── test_seed.py │ └── test_tracker.py ├── tracker.py └── utils.py ├── tractanalysis ├── __init__.py ├── afd_along_streamlines.py ├── bingham_metric_along_streamlines.py ├── bundle_operations.py ├── connectivity_segmentation.py ├── distance_to_centroid.py ├── fibertube_scoring.py ├── fixel_density.py ├── json_utils.py ├── mrds_along_streamlines.py ├── multi_bundle_operations.py ├── reproducibility_measures.py ├── scoring.py ├── streamlines_metrics.pyx ├── tests │ ├── test_afd_along_streamlines.py │ ├── test_fixel_density.py │ ├── test_json_utils.py │ ├── test_reproducibility_measures.py │ └── test_voxel_boundary_intersection.py ├── todi.py ├── todi_util.py └── voxel_boundary_intersection.pyx ├── tractograms ├── __init__.py ├── dps_and_dpp_management.py ├── intersection_finder.py ├── lazy_tractogram_operations.py ├── streamline_and_mask_operations.py ├── streamline_operations.py ├── tests │ ├── __init__.py │ ├── test_dps_and_dpp_management.py │ ├── test_lazy_tractogram_operations.py │ ├── test_streamline_and_mask_operations.py │ ├── test_streamline_operations.py │ └── test_tractogram_operations.py ├── tractogram_operations.py └── uncompress.pyx ├── utils ├── __init__.py ├── filenames.py ├── metrics_tools.py ├── scilpy_bot.py ├── spatial.py └── tests │ └── test_scilpy_bot.py ├── version.py └── viz ├── __init__.py ├── backends ├── __init__.py ├── fury.py ├── pil.py └── vtk.py ├── color.py ├── gradients.py ├── legacy ├── __init__.py └── 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