Modules

• scilpy.connectivity package
  • scilpy.connectivity.connectivity_tools module
• scilpy.denoise package
  • scilpy.denoise.asym_filtering module
    • cosine_filtering()
    • unified_filtering()
• scilpy.dwi package
  • scilpy.dwi.operations module
    • apply_bias_field()
    • compute_dwi_attenuation()
    • compute_residuals()
    • compute_residuals_statistics()
    • detect_volume_outliers()
  • scilpy.dwi.utils module
    • extract_b0()
    • extract_dwi_shell()
• scilpy.gpuparallel package
  • scilpy.gpuparallel.opencl_utils module
    • CLKernel
      • CLKernel.code_string
      • CLKernel.entry_point
      • CLKernel.set_define()
    • CLManager
      • CLManager.OutBuffer
      • CLManager.add_input_buffer()
      • CLManager.add_output_buffer()
      • CLManager.run()
      • CLManager.update_input_buffer()
      • CLManager.update_output_buffer()
    • cl_device_type()
• scilpy.gradients package
  • scilpy.gradients.bvec_bval_tools module
    • B0ExtractionStrategy
      • B0ExtractionStrategy.ALL
      • B0ExtractionStrategy.FIRST
      • B0ExtractionStrategy.MEAN
    • check_b0_threshold()
    • flip_gradient_sampling()
    • identify_shells()
    • is_normalized_bvecs()
    • normalize_bvecs()
    • round_bvals_to_shell()
    • str_to_axis_index()
    • swap_gradient_axis()
  • scilpy.gradients.gen_gradient_sampling module
    • energy_comparison()
    • generate_gradient_sampling()
  • scilpy.gradients.optimize_gradient_sampling module
    • add_b0s_to_bvecs()
    • compute_bvalue_lin_b()
    • compute_bvalue_lin_q()
    • compute_min_duty_cycle_bruteforce()
    • compute_peak_power()
    • correct_b0s_philips()
    • swap_sampling_eddy()
  • scilpy.gradients.utils module
    • get_new_gtab_order()
    • random_uniform_on_sphere()
• scilpy.image package
  • scilpy.image.labels module
    • combine_labels()
    • dilate_labels()
    • get_binary_mask_from_labels()
    • get_data_as_labels()
    • get_labels_from_mask()
    • get_lut_dir()
    • get_stats_in_label()
    • load_wmparc_labels()
    • merge_labels_into_mask()
    • remove_labels()
    • split_labels()
  • scilpy.image.reslice module
    • reslice()
  • scilpy.image.utils module
    • check_slice_indices()
    • compute_nifti_bounding_box()
    • extract_affine()
    • split_mask_blobs_kmeans()
    • volume_iterator()
  • scilpy.image.volume_math module
    • absolute_value()
    • addition()
    • around()
    • base_10_log()
    • ceil()
    • closing()
    • concatenate()
    • convert()
    • difference()
    • dilation()
    • division()
    • erosion()
    • floor()
    • gaussian_blur()
    • get_array_ops()
    • get_image_ops()
    • get_operations_doc()
    • intersection()
    • invert()
    • lower_clip()
    • lower_threshold()
    • lower_threshold_eq()
    • lower_threshold_otsu()
    • mean()
    • multiplication()
    • natural_log()
    • neighborhood_correlation()
    • neighborhood_correlation_()
    • normalize_max()
    • normalize_sum()
    • opening()
    • std()
    • subtraction()
    • union()
    • upper_clip()
    • upper_threshold()
    • upper_threshold_eq()
    • upper_threshold_otsu()
  • scilpy.image.volume_operations module
    • apply_transform()
    • compute_distance_map()
    • compute_nawm()
    • compute_snr()
    • count_non_zero_voxels()
    • crop_volume()
    • flip_volume()
    • mask_data_with_default_cube()
    • merge_metrics()
    • normalize_metric()
    • register_image()
    • remove_outliers_ransac()
    • resample_volume()
    • reshape_volume()
    • smooth_to_fwhm()
    • transform_dwi()
  • scilpy.image.volume_space_management module
• scilpy.io package
  • scilpy.io.btensor module
    • convert_bdelta_to_bshape()
    • convert_bshape_to_bdelta()
    • generate_btensor_input()
  • scilpy.io.deprecator module
    • ScilpyExpiredDeprecation
    • deprecate_script()
  • scilpy.io.fetcher module
    • download_file_from_google_drive()
    • fetch_data()
    • get_synb0_template_path()
    • get_testing_files_dict()
  • scilpy.io.gradients module
    • fsl2mrtrix()
    • mrtrix2fsl()
    • save_gradient_sampling_fsl()
    • save_gradient_sampling_mrtrix()
  • scilpy.io.image module
    • assert_same_resolution()
    • get_data_as_mask()
    • load_img()
  • scilpy.io.streamlines module
    • check_tracts_same_format()
    • ichunk()
    • is_argument_set()
    • load_dpp_files_as_dpp()
    • load_dps_files_as_dps()
    • load_tractogram_with_reference()
    • reconstruct_streamlines()
    • reconstruct_streamlines_from_memmap()
    • save_tractogram()
    • streamlines_to_memmap()
    • verify_compatibility_with_reference_sft()
  • scilpy.io.tensor module
    • convert_tensor_format()
    • convert_tensor_from_dipy_format()
    • convert_tensor_to_dipy_format()
  • scilpy.io.utils module
    • add_b0_thresh_arg()
    • add_bbox_arg()
    • add_compression_arg()
    • add_default_screenshot_args()
    • add_json_args()
    • add_labelmap_screenshot_args()
    • add_overlays_screenshot_args()
    • add_overwrite_arg()
    • add_peaks_screenshot_args()
    • add_precision_arg()
    • add_processes_arg()
    • add_reference_arg()
    • add_sh_basis_args()
    • add_skip_b0_check_arg()
    • add_sphere_arg()
    • add_tolerance_arg()
    • add_verbose_arg()
    • add_volume_screenshot_args()
    • assert_fsl_options_exist()
    • assert_gradients_filenames_valid()
    • assert_headers_compatible()
    • assert_inputs_dirs_exist()
    • assert_inputs_exist()
    • assert_output_dirs_exist_and_empty()
    • assert_outputs_exist()
    • assert_overlay_colors()
    • assert_roi_radii_format()
    • check_tract_trk()
    • check_tracts_same_format()
    • get_acq_parameters()
    • get_default_screenshotting_data()
    • link_bundles_and_reference()
    • load_matrix_in_any_format()
    • parse_sh_basis_arg()
    • parser_color_type()
    • ranged_type()
    • read_info_from_mb_bdo()
    • redirect_stdout_c()
    • save_matrix_in_any_format()
    • validate_nbr_processes()
    • validate_sh_basis_choice()
    • verify_compression_th()
  • scilpy.io.varian_fdf module
    • add_gradient_info()
    • correct_procpar_intensity()
    • format_raw_header()
    • get_gain()
    • load_fdf()
    • read_directory()
    • read_file()
    • save_babel()
    • write_gradient_information()
• scilpy.preprocessing package
  • scilpy.preprocessing.distortion_correction module
    • create_acqparams()
    • create_index()
    • create_multi_topup_index()
    • create_non_zero_norm_bvecs()
• scilpy.reconst package
  • scilpy.reconst.aodf module
    • compute_asymmetry_index()
    • compute_odd_power_map()
  • scilpy.reconst.bingham module
    • BinghamDistribution
      • BinghamDistribution.evaluate()
      • BinghamDistribution.get_flatten()
      • BinghamDistribution.peak_direction()
    • bingham_fit_sh()
    • bingham_to_peak_direction()
    • bingham_to_sf()
    • compute_fiber_density()
    • compute_fiber_fraction()
    • compute_fiber_spread()
  • scilpy.reconst.divide module
    • fit_gamma()
    • gamma_fit2metrics()
  • scilpy.reconst.fiber_coherence module
    • compute_coherence_table_for_transforms()
    • compute_fiber_coherence()
  • scilpy.reconst.fodf module
    • fit_from_model()
    • get_ventricles_max_fodf()
    • verify_failed_voxels_shm_coeff()
    • verify_frf_files()
  • scilpy.reconst.frf module
    • compute_msmt_frf()
    • compute_ssst_frf()
    • replace_frf()
  • scilpy.reconst.mti module
    • adjust_B1_map_header()
    • adjust_B1_map_intensities()
    • apply_B1_corr_empiric()
    • apply_B1_corr_model_based()
    • compute_ratio_map()
    • compute_saturation_map()
    • process_contrast_map()
    • py_fspecial_gauss()
    • smooth_B1_map()
    • threshold_map()
  • scilpy.reconst.sh module
    • compute_rish()
    • compute_sh_coefficients()
    • convert_sh_basis()
    • convert_sh_to_sf()
    • maps_from_sh()
    • peaks_from_sh()
    • verify_data_vs_sh_order()
  • scilpy.reconst.utils module
    • find_order_from_nb_coeff()
    • get_maximas()
    • get_sh_order_and_fullness()
    • get_sphere_neighbours()
• scilpy.segment package
  • scilpy.segment.models module
    • remove_similar_streamlines()
  • scilpy.segment.recobundlesx module
    • RecobundlesX
      • RecobundlesX.cleanup()
      • RecobundlesX.get_final_pruned_indices()
      • RecobundlesX.prune_far_from_model()
      • RecobundlesX.recognize()
  • scilpy.segment.streamlines module
    • filter_cuboid()
    • filter_ellipsoid()
    • filter_grid_roi()
    • filter_grid_roi_both()
    • pre_filtering_for_geometrical_shape()
    • streamlines_in_mask()
  • scilpy.segment.tractogram_from_roi module
    • compute_endpoint_masks()
    • compute_masks_from_bundles()
    • segment_tractogram_from_roi()
  • scilpy.segment.voting_scheme module
    • VotingScheme
    • single_recognize()
    • single_recognize_parallel()
• scilpy.stats package
  • scilpy.stats.matrix_stats module
  • scilpy.stats.stats module
    • verify_group_difference()
    • verify_homoscedasticity()
    • verify_normality()
    • verify_post_hoc()
  • scilpy.stats.utils module
    • data_for_stat
      • data_for_stat.data_dictionnary
      • data_for_stat.get_bundles_list()
      • data_for_stat.get_data_sample()
      • data_for_stat.get_first_bundle()
      • data_for_stat.get_first_metric()
      • data_for_stat.get_first_participant()
      • data_for_stat.get_groups_dictionnary()
      • data_for_stat.get_groups_list()
      • data_for_stat.get_metrics_list()
      • data_for_stat.get_participant_attributes_list()
      • data_for_stat.get_participants_list()
      • data_for_stat.get_values_list()
      • data_for_stat.validation_participant_id()
    • get_group_data_sample()
    • visualise_distribution()
    • write_csv_from_json()
    • write_current_dictionnary()
• scilpy.surfaces package
  • scilpy.surfaces.surface_operations module
    • apply_transform()
    • flip()
  • scilpy.surfaces.utils module
    • convert_freesurfer_into_polydata()
    • flip_surfaces_axes()
• scilpy.tracking package
  • scilpy.tracking.propagator module
  • scilpy.tracking.seed module
  • scilpy.tracking.tracker module
  • scilpy.tracking.utils module
    • TrackingDirection
    • add_mandatory_options_tracking()
    • add_out_options()
    • add_seeding_options()
    • add_tracking_options()
    • add_tracking_ptt_options()
    • get_direction_getter()
    • get_theta()
    • sample_distribution()
    • save_tractogram()
    • tqdm_if_verbose()
    • verify_seed_options()
    • verify_streamline_length_options()
• scilpy.tractanalysis package
  • scilpy.tractanalysis.afd_along_streamlines module
    • afd_and_rd_sums_along_streamlines()
    • afd_map_along_streamlines()
  • scilpy.tractanalysis.bingham_metric_along_streamlines module
    • bingham_metric_map_along_streamlines()
    • bingham_metric_sum_along_streamlines()
  • scilpy.tractanalysis.distance_to_centroid module
    • min_dist_to_centroid()
  • scilpy.tractanalysis.features module
  • scilpy.tractanalysis.voxel_boundary_intersection module
    • subdivide_streamlines_at_voxel_faces()
  • scilpy.tractanalysis.json_utils module
    • average_dict()
    • merge_dict()
  • scilpy.tractanalysis.reproducibility_measures module
  • scilpy.tractanalysis.scoring module
  • scilpy.tractanalysis.streamlines_metrics module
    • compute_tract_counts_map()
  • scilpy.tractanalysis.todi_util module
    • compute_vectors_norm()
    • generate_mask_indices_1d()
    • get_dir_to_sphere_id()
    • get_indices_1d()
    • get_segments_dir_and_norm()
    • get_segments_mid_pts_positions()
    • get_segments_vectors()
    • get_vectors_dir_and_norm()
    • get_vectors_dir_and_norm_rel_to_center()
    • normalize_vectors()
    • p_normalize_vectors()
    • psf_from_sphere()
    • streamlines_to_endpoints()
    • streamlines_to_pts_dir_norm()
    • streamlines_to_segments()
  • scilpy.tractanalysis.todi module
    • TrackOrientationDensityImaging
      • TrackOrientationDensityImaging.compute_average_dir()
      • TrackOrientationDensityImaging.compute_distance_to_peak()
      • TrackOrientationDensityImaging.compute_todi()
      • TrackOrientationDensityImaging.get_mask()
      • TrackOrientationDensityImaging.get_sh()
      • TrackOrientationDensityImaging.get_tdi()
      • TrackOrientationDensityImaging.get_todi()
      • TrackOrientationDensityImaging.get_todi_shape()
      • TrackOrientationDensityImaging.mask_todi()
      • TrackOrientationDensityImaging.normalize_todi_per_voxel()
      • TrackOrientationDensityImaging.reshape_to_3d()
      • TrackOrientationDensityImaging.set_todi()
      • TrackOrientationDensityImaging.smooth_todi_dir()
      • TrackOrientationDensityImaging.smooth_todi_spatial()
  • scilpy.tractanalysis.tools module
• scilpy.tractograms package
  • scilpy.tractograms.dps_and_dpp_management module
    • add_data_as_color_dpp()
    • convert_dps_to_dpp()
    • perform_correlation_on_endpoints()
    • perform_operation_dpp_to_dps()
    • perform_operation_on_dpp()
    • project_dpp_to_map()
    • project_map_to_streamlines()
  • scilpy.tractograms.lazy_tractogram_operations module
    • lazy_concatenate()
    • lazy_streamlines_count()
  • scilpy.tractograms.streamline_and_mask_operations module
  • scilpy.tractograms.tractogram_operations module
  • scilpy.tractograms.uncompress module
• scilpy.utils package
  • scilpy.utils.filenames module
    • add_filename_suffix()
    • split_name_with_nii()
  • scilpy.utils.metrics_tools module
    • compute_lesion_stats()
    • get_bundle_metrics_mean_std()
    • get_bundle_metrics_mean_std_per_point()
    • get_bundle_metrics_profiles()
    • weighted_mean_std()
  • scilpy.utils.streamlines module
  • scilpy.utils.util module
• scilpy.viz package
  • scilpy.viz.chord_chart module
  • scilpy.viz.gradient_sampling module
  • scilpy.viz.scene_utils module
  • scilpy.viz.screenshot module
  • scilpy.viz.utils module
    • affine_from_offset()
    • check_mosaic_layout()
    • compute_cell_topleft_pos()