.python-version
LICENSE
MANIFEST.in
README.md
requirements.txt
setup.py
data/LUT/dk_aggregate_structures.json
data/LUT/freesurfer_desikan_killiany.json
data/LUT/freesurfer_subcortical.json
scilpy/__init__.py
scilpy/version.py
scilpy.egg-info/PKG-INFO
scilpy.egg-info/SOURCES.txt
scilpy.egg-info/dependency_links.txt
scilpy.egg-info/entry_points.txt
scilpy.egg-info/requires.txt
scilpy.egg-info/top_level.txt
scilpy/connectivity/__init__.py
scilpy/connectivity/utils.py
scilpy/denoise/__init__.py
scilpy/denoise/asym_averaging.py
scilpy/denoise/bilateral_filtering.py
scilpy/direction/__init__.py
scilpy/direction/peaks.py
scilpy/gpuparallel/__init__.py
scilpy/gpuparallel/opencl_utils.py
scilpy/gradientsampling/__init__.py
scilpy/gradientsampling/gen_gradient_sampling.py
scilpy/gradientsampling/multiple_shell_energy.py
scilpy/gradientsampling/optimize_gradient_sampling.py
scilpy/gradientsampling/save_gradient_sampling.py
scilpy/image/__init__.py
scilpy/image/datasets.py
scilpy/image/labels.py
scilpy/image/operations.py
scilpy/image/resample_volume.py
scilpy/image/reslice.py
scilpy/image/utils.py
scilpy/image/tests/__init__.py
scilpy/image/tests/test_labels.py
scilpy/io/__init__.py
scilpy/io/fetcher.py
scilpy/io/image.py
scilpy/io/streamlines.py
scilpy/io/utils.py
scilpy/io/varian_fdf.py
scilpy/preprocessing/__init__.py
scilpy/preprocessing/distortion_correction.py
scilpy/reconst/__init__.py
scilpy/reconst/afd_along_streamlines.py
scilpy/reconst/b_tensor_utils.py
scilpy/reconst/bingham.py
scilpy/reconst/divide_fit.py
scilpy/reconst/dti.py
scilpy/reconst/fiber_coherence.py
scilpy/reconst/fodf.py
scilpy/reconst/frf.py
scilpy/reconst/lobe_metrics_along_streamlines.py
scilpy/reconst/multi_processes.py
scilpy/reconst/raw_signal.py
scilpy/reconst/sh.py
scilpy/reconst/utils.py
scilpy/segment/__init__.py
scilpy/segment/models.py
scilpy/segment/recobundlesx.py
scilpy/segment/streamlines.py
scilpy/segment/tractogram_from_roi.py
scilpy/segment/voting_scheme.py
scilpy/stats/__init__.py
scilpy/stats/stats.py
scilpy/stats/utils.py
scilpy/tracking/__init__.py
scilpy/tracking/propagator.py
scilpy/tracking/seed.py
scilpy/tracking/tools.py
scilpy/tracking/tracker.py
scilpy/tracking/utils.py
scilpy/tractanalysis/__init__.py
scilpy/tractanalysis/distance_to_centroid.py
scilpy/tractanalysis/features.py
scilpy/tractanalysis/grid_intersections.pyx
scilpy/tractanalysis/quick_tools.pyx
scilpy/tractanalysis/reproducibility_measures.py
scilpy/tractanalysis/scoring.py
scilpy/tractanalysis/streamlines_metrics.pyx
scilpy/tractanalysis/todi.py
scilpy/tractanalysis/todi_util.py
scilpy/tractanalysis/tools.py
scilpy/tractanalysis/uncompress.pyx
scilpy/tractograms/__init__.py
scilpy/tractograms/lazy_tractogram_operations.py
scilpy/tractograms/tractogram_operations.py
scilpy/utils/__init__.py
scilpy/utils/bvec_bval_tools.py
scilpy/utils/filenames.py
scilpy/utils/image.py
scilpy/utils/metrics_tools.py
scilpy/utils/streamlines.py
scilpy/utils/util.py
scilpy/viz/__init__.py
scilpy/viz/chord_chart.py
scilpy/viz/gradient_sampling.py
scilpy/viz/scene_utils.py
scilpy/viz/screenshot.py
scilpy/viz/utils.py
scripts/__init__.py
scripts/scil_add_tracking_mask_to_pft_maps.py
scripts/scil_analyse_lesions_load.py
scripts/scil_apply_bias_field_on_dwi.py
scripts/scil_apply_transform_to_bvecs.py
scripts/scil_apply_transform_to_hdf5.py
scripts/scil_apply_transform_to_image.py
scripts/scil_apply_transform_to_surface.py
scripts/scil_apply_transform_to_tractogram.py
scripts/scil_assign_custom_color_to_tractogram.py
scripts/scil_assign_uniform_color_to_tractograms.py
scripts/scil_clean_qbx_clusters.py
scripts/scil_combine_labels.py
scripts/scil_compare_connectivity.py
scripts/scil_compress_streamlines.py
scripts/scil_compute_MT_maps.py
scripts/scil_compute_NODDI.py
scripts/scil_compute_NODDI_priors.py
scripts/scil_compute_asym_odf_metrics.py
scripts/scil_compute_bundle_mean_std.py
scripts/scil_compute_bundle_mean_std_per_point.py
scripts/scil_compute_bundle_volume.py
scripts/scil_compute_bundle_volume_per_label.py
scripts/scil_compute_bundle_voxel_label_map.py
scripts/scil_compute_centroid.py
scripts/scil_compute_connectivity.py
scripts/scil_compute_divide.py
scripts/scil_compute_dti_metrics.py
scripts/scil_compute_endpoints_map.py
scripts/scil_compute_fodf_max_in_ventricles.py
scripts/scil_compute_fodf_metrics.py
scripts/scil_compute_freewater.py
scripts/scil_compute_hdf5_average_density_map.py
scripts/scil_compute_ihMT_maps.py
scripts/scil_compute_kurtosis_metrics.py
scripts/scil_compute_lobe_specific_fodf_metrics.py
scripts/scil_compute_local_tracking.py
scripts/scil_compute_local_tracking_dev.py
scripts/scil_compute_local_tracking_gpu.py
scripts/scil_compute_maps_for_particle_filter_tracking.py
scripts/scil_compute_mean_fixel_afd_from_bundles.py
scripts/scil_compute_mean_fixel_afd_from_hdf5.py
scripts/scil_compute_mean_fixel_lobe_metric_from_bundles.py
scripts/scil_compute_mean_frf.py
scripts/scil_compute_memsmt_fodf.py
scripts/scil_compute_memsmt_frf.py
scripts/scil_compute_metrics_stats_in_ROI.py
scripts/scil_compute_msmt_fodf.py
scripts/scil_compute_msmt_frf.py
scripts/scil_compute_pca.py
scripts/scil_compute_pft.py
scripts/scil_compute_powder_average.py
scripts/scil_compute_qball_metrics.py
scripts/scil_compute_qbx.py
scripts/scil_compute_rish_from_sh.py
scripts/scil_compute_seed_by_labels.py
scripts/scil_compute_seed_density_map.py
scripts/scil_compute_sf_from_sh.py
scripts/scil_compute_sh_from_signal.py
scripts/scil_compute_ssst_fodf.py
scripts/scil_compute_ssst_frf.py
scripts/scil_compute_streamlines_density_map.py
scripts/scil_compute_streamlines_length_stats.py
scripts/scil_compute_todi.py
scripts/scil_concatenate_dwi.py
scripts/scil_connectivity_math.py
scripts/scil_convert_fdf.py
scripts/scil_convert_gradients_fsl_to_mrtrix.py
scripts/scil_convert_gradients_mrtrix_to_fsl.py
scripts/scil_convert_json_to_xlsx.py
scripts/scil_convert_rgb.py
scripts/scil_convert_sh_basis.py
scripts/scil_convert_surface.py
scripts/scil_convert_tensors.py
scripts/scil_convert_tractogram.py
scripts/scil_count_non_zero_voxels.py
scripts/scil_count_streamlines.py
scripts/scil_crop_volume.py
scripts/scil_cut_streamlines.py
scripts/scil_decompose_connectivity.py
scripts/scil_detect_dwi_volume_outliers.py
scripts/scil_detect_streamlines_loops.py
scripts/scil_dilate_labels.py
scripts/scil_estimate_bundles_diameter.py
scripts/scil_evaluate_bundles_binary_classification_measures.py
scripts/scil_evaluate_bundles_individual_measures.py
scripts/scil_evaluate_bundles_pairwise_agreement_measures.py
scripts/scil_evaluate_connectivity_graph_measures.py
scripts/scil_evaluate_connectivity_pairwise_agreement_measures.py
scripts/scil_execute_angle_aware_bilateral_filtering.py
scripts/scil_execute_asymmetric_filtering.py
scripts/scil_extract_b0.py
scripts/scil_extract_dwi_shell.py
scripts/scil_extract_ushape.py
scripts/scil_filter_connectivity.py
scripts/scil_filter_streamlines_by_length.py
scripts/scil_filter_streamlines_by_orientation.py
scripts/scil_filter_tractogram.py
scripts/scil_filter_tractogram_anatomically.py
scripts/scil_fit_bingham_to_fodf.py
scripts/scil_fix_dsi_studio_trk.py
scripts/scil_flip_gradients.py
scripts/scil_flip_streamlines.py
scripts/scil_flip_surface.py
scripts/scil_flip_volume.py
scripts/scil_generate_gradient_sampling.py
scripts/scil_generate_priors_from_bundle.py
scripts/scil_group_comparison.py
scripts/scil_image_math.py
scripts/scil_merge_json.py
scripts/scil_merge_sh.py
scripts/scil_normalize_connectivity.py
scripts/scil_outlier_rejection.py
scripts/scil_perform_majority_vote.py
scripts/scil_plot_mean_std_per_point.py
scripts/scil_prepare_eddy_command.py
scripts/scil_prepare_topup_command.py
scripts/scil_print_connectivity_filenames.py
scripts/scil_print_header.py
scripts/scil_project_streamlines_to_map.py
scripts/scil_recognize_multi_bundles.py
scripts/scil_recognize_single_bundle.py
scripts/scil_register_tractogram.py
scripts/scil_remove_invalid_streamlines.py
scripts/scil_remove_labels.py
scripts/scil_remove_outliers_ransac.py
scripts/scil_remove_similar_streamlines.py
scripts/scil_reorder_connectivity.py
scripts/scil_reorder_dwi_philips.py
scripts/scil_resample_bvals.py
scripts/scil_resample_streamlines.py
scripts/scil_resample_tractogram.py
scripts/scil_resample_volume.py
scripts/scil_reshape_to_reference.py
scripts/scil_run_commit.py
scripts/scil_run_nlmeans.py
scripts/scil_save_connections_from_hdf5.py
scripts/scil_score_bundles.py
scripts/scil_score_tractogram.py
scripts/scil_screenshot_bundle.py
scripts/scil_screenshot_dti.py
scripts/scil_screenshot_volume_mosaic_overlap.py
scripts/scil_search_keywords.py
scripts/scil_set_response_function.py
scripts/scil_shuffle_streamlines.py
scripts/scil_smooth_streamlines.py
scripts/scil_smooth_surface.py
scripts/scil_snr_in_roi.py
scripts/scil_split_image.py
scripts/scil_split_tractogram.py
scripts/scil_split_volume_by_ids.py
scripts/scil_split_volume_by_labels.py
scripts/scil_streamlines_math.py
scripts/scil_swap_gradient_axis.py
scripts/scil_tractogram_math.py
scripts/scil_uniformize_streamlines_endpoints.py
scripts/scil_validate_and_correct_bvecs.py
scripts/scil_validate_and_correct_eddy_gradients.py
scripts/scil_validate_bids.py
scripts/scil_verify_space_attributes_compatibility.py
scripts/scil_visualize_bingham_fit.py
scripts/scil_visualize_bundles.py
scripts/scil_visualize_bundles_mosaic.py
scripts/scil_visualize_connectivity.py
scripts/scil_visualize_fodf.py
scripts/scil_visualize_gradients.py
scripts/scil_visualize_histogram.py
scripts/scil_visualize_scatterplot.py
scripts/scil_visualize_seeds.py
scripts/scil_visualize_seeds_3d.py
scripts/tests/__init__.py
scripts/tests/test_add_tracking_mask_to_pft_maps.py
scripts/tests/test_apply_bias_field_on_dwi.py
scripts/tests/test_apply_transform_to_bvecs.py
scripts/tests/test_apply_transform_to_hdf5.py
scripts/tests/test_apply_transform_to_image.py
scripts/tests/test_apply_transform_to_surface.py
scripts/tests/test_apply_transform_to_tractogram.py
scripts/tests/test_assign_custom_color_to_tractogram.py
scripts/tests/test_assign_uniform_color_to_tractograms.py
scripts/tests/test_clean_qbx_clusters.py
scripts/tests/test_combine_labels.py
scripts/tests/test_compare_connectivity.py
scripts/tests/test_compress_streamlines.py
scripts/tests/test_compute_MT_maps.py
scripts/tests/test_compute_NODDI.py
scripts/tests/test_compute_NODDI_priors.py
scripts/tests/test_compute_asym_odf_metrics.py
scripts/tests/test_compute_bundle_mean_std.py
scripts/tests/test_compute_bundle_mean_std_per_point.py
scripts/tests/test_compute_bundle_volume.py
scripts/tests/test_compute_bundle_volume_per_label.py
scripts/tests/test_compute_bundle_voxel_label_map.py
scripts/tests/test_compute_centroid.py
scripts/tests/test_compute_connectivity.py
scripts/tests/test_compute_divide.py
scripts/tests/test_compute_dti_metrics.py
scripts/tests/test_compute_endpoints_map.py
scripts/tests/test_compute_fodf_max_in_ventricles.py
scripts/tests/test_compute_fodf_metrics.py
scripts/tests/test_compute_freewater.py
scripts/tests/test_compute_hdf5_average_density_map.py
scripts/tests/test_compute_ihMT_maps.py
scripts/tests/test_compute_kurtosis_metrics.py
scripts/tests/test_compute_lobe_specific_fodf_metrics.py
scripts/tests/test_compute_local_tracking.py
scripts/tests/test_compute_local_tracking_dev.py
scripts/tests/test_compute_local_tracking_gpu.py
scripts/tests/test_compute_maps_for_particle_filter_tracking.py
scripts/tests/test_compute_mean_fixel_afd_from_bundles.py
scripts/tests/test_compute_mean_fixel_afd_from_hdf5.py
scripts/tests/test_compute_mean_fixel_lobe_metric_from_bundles.py
scripts/tests/test_compute_mean_frf.py
scripts/tests/test_compute_memsmt_fodf.py
scripts/tests/test_compute_memsmt_frf.py
scripts/tests/test_compute_metrics_stats_in_ROI.py
scripts/tests/test_compute_msmt_fodf.py
scripts/tests/test_compute_msmt_frf.py
scripts/tests/test_compute_pca.py
scripts/tests/test_compute_pft.py
scripts/tests/test_compute_powder_average.py
scripts/tests/test_compute_qball_metrics.py
scripts/tests/test_compute_qbx.py
scripts/tests/test_compute_rish_from_sh.py
scripts/tests/test_compute_seed_by_labels.py
scripts/tests/test_compute_seed_density_map.py
scripts/tests/test_compute_sf_from_sh.py
scripts/tests/test_compute_sh_from_signal.py
scripts/tests/test_compute_ssst_fodf.py
scripts/tests/test_compute_ssst_frf.py
scripts/tests/test_compute_streamlines_density_map.py
scripts/tests/test_compute_streamlines_length_stats.py
scripts/tests/test_compute_todi.py
scripts/tests/test_concatenate_dwi.py
scripts/tests/test_connectivity_math.py
scripts/tests/test_convert_fdf.py
scripts/tests/test_convert_gradients_fsl_to_mrtrix.py
scripts/tests/test_convert_gradients_mrtrix_to_fsl.py
scripts/tests/test_convert_json_to_xlsx.py
scripts/tests/test_convert_rgb.py
scripts/tests/test_convert_sh_basis.py
scripts/tests/test_convert_surface.py
scripts/tests/test_convert_tensors.py
scripts/tests/test_convert_tractogram.py
scripts/tests/test_count_non_zero_voxels.py
scripts/tests/test_count_streamlines.py
scripts/tests/test_crop_volume.py
scripts/tests/test_cut_streamlines.py
scripts/tests/test_decompose_connectivity.py
scripts/tests/test_detect_streamlines_loops.py
scripts/tests/test_dilate_labels.py
scripts/tests/test_estimate_bundles_diameter.py
scripts/tests/test_evaluate_bundles_binary_classification_measures.py
scripts/tests/test_evaluate_bundles_individual_measures.py
scripts/tests/test_evaluate_bundles_pairwise_agreement_measures.py
scripts/tests/test_evaluate_connectivity_graph_measures.py
scripts/tests/test_evaluate_connectivity_pairwise_agreement_measures.py
scripts/tests/test_execute_angle_aware_bilateral_filtering.py
scripts/tests/test_execute_asymmetric_filtering.py
scripts/tests/test_extract_b0.py
scripts/tests/test_extract_dwi_shell.py
scripts/tests/test_extract_ushape.py
scripts/tests/test_filter_connectivity.py
scripts/tests/test_filter_streamlines_by_length.py
scripts/tests/test_filter_streamlines_by_orientation.py
scripts/tests/test_filter_tractogram.py
scripts/tests/test_filter_tractogram_anatomically.py
scripts/tests/test_fit_bingham_to_fodf.py
scripts/tests/test_fix_dsi_studio_trk.py
scripts/tests/test_flip_gradients.py
scripts/tests/test_flip_streamlines.py
scripts/tests/test_flip_surface.py
scripts/tests/test_flip_volume.py
scripts/tests/test_generate_gradient_sampling.py
scripts/tests/test_generate_priors_from_bundle.py
scripts/tests/test_group_comparison.py
scripts/tests/test_image_math.py
scripts/tests/test_merge_json.py
scripts/tests/test_merge_sh.py
scripts/tests/test_normalize_connectivity.py
scripts/tests/test_outlier_rejection.py
scripts/tests/test_perform_majority_vote.py
scripts/tests/test_plot_mean_std_per_point.py
scripts/tests/test_prepare_eddy_command.py
scripts/tests/test_prepare_topup_command.py
scripts/tests/test_print_connectivity_filenames.py
scripts/tests/test_print_header.py
scripts/tests/test_project_streamlines_to_map.py
scripts/tests/test_recognize_multi_bundles.py
scripts/tests/test_recognize_single_bundle.py
scripts/tests/test_register_tractogram.py
scripts/tests/test_remove_invalid_streamlines.py
scripts/tests/test_remove_labels.py
scripts/tests/test_remove_outliers_ransac.py
scripts/tests/test_reorder_connectivity.py
scripts/tests/test_reorder_dwi_philips.py
scripts/tests/test_resample_bvals.py
scripts/tests/test_resample_streamlines.py
scripts/tests/test_resample_tractogram.py
scripts/tests/test_resample_volume.py
scripts/tests/test_reshape_to_reference.py
scripts/tests/test_run_commit.py
scripts/tests/test_run_nlmeans.py
scripts/tests/test_save_connections_from_hdf5.py
scripts/tests/test_score_bundles.py
scripts/tests/test_score_tractogram.py
scripts/tests/test_screenshot_bundle.py
scripts/tests/test_screenshot_dti.py
scripts/tests/test_screenshot_volume_mosaic_overlap.py
scripts/tests/test_search_keywords.py
scripts/tests/test_set_response_function.py
scripts/tests/test_shuffle_streamlines.py
scripts/tests/test_smooth_streamlines.py
scripts/tests/test_smooth_surface.py
scripts/tests/test_snr_in_roi.py
scripts/tests/test_split_image.py
scripts/tests/test_split_tractogram.py
scripts/tests/test_split_volume_by_ids.py
scripts/tests/test_split_volume_by_labels.py
scripts/tests/test_streamlines_math.py
scripts/tests/test_swap_gradient_axis.py
scripts/tests/test_tractogram_math.py
scripts/tests/test_uniformize_streamlines_endpoints.py
scripts/tests/test_validate_and_correct_bvecs.py
scripts/tests/test_validate_and_correct_eddy_gradients.py
scripts/tests/test_validate_bids.py
scripts/tests/test_verify_space_attributes_compatibility.py
scripts/tests/test_visualize_bingham_fit.py
scripts/tests/test_visualize_bundles.py
scripts/tests/test_visualize_bundles_mosaic.py
scripts/tests/test_visualize_connectivity.py
scripts/tests/test_visualize_fodf.py
scripts/tests/test_visualize_gradients.py
scripts/tests/test_visualize_histogram.py
scripts/tests/test_visualize_scatterplot.py
scripts/tests/test_visualize_seeds.py
scripts/tests/test_visualize_seeds_3d.py