scilpy

Getting started

  • Getting ready for tutorials
    • Installation
    • Download data

Documentation & Tutorials

  • 1. Manipulating volumes
    • Cropping volumes
  • 2. Reconstructing the local model
    • Single-shell single-tissue fODF (ssst-fODF)
      • Preparing data for this tutorial
      • 1. Computing the frf
      • 2. Computing the fODF
      • 3. Visualizing the fODF
    • Multi-shell multi-tissue fODF (msmt-fODF)
      • Preparing data for this tutorial
      • 1. Computing the frf
      • 2. Computing the fODF
      • 3. Visualizing the fODF
      • References
    • Multi-encoding multi-shell multi-tissue fODF (memsmt-fODF)
      • Preparing data for this tutorial
      • 1. Computing the frf
      • 2. Computing the fODF
      • 3. Visualizing the fODF
      • References
    • Asymmetric orientation distribution functions (aodf)
      • Preparing data for this tutorial
      • 1. Creating the aodf
      • 2. Computing metrics
    • Estimate Q-ball orientation distribution functions
      • Preparing data for this tutorial
      • Running Q-ball
    • Generating Myelin Indices Maps using Magnetization Transfer Imaging (MTI)
      • Understanding the output
      • Understanding the input
        • Acquisition Parameters
      • Preparing data for this tutorial
      • Step-by-step processing
        • Basic Usage
        • Similar Script: scil_mti_maps_MT
        • When to use each script
      • To go further
        • B1+ Field Correction (Optional)
        • Additional Options
      • Using in workflows
        • Workflow available: ihmt_flow
      • References
    • Tensor-valued dMRI metrics reconstruction using DIVIDE
      • Preparing data for this tutorial
      • Computing b-tensor metrics
      • References
  • 3. Performing tractography
    • Local Tracking with DIPY
    • Tracking in developer mode!
    • Introduction to the Fibertube Tracking
      • Terminology
      • Methodology
      • Preparing the data
      • Visualising collisions
      • Fibertube metrics
      • Performing fibertube tracking
        • Seeding
        • Tracking
        • Reconstruction analysis
  • 4. Tractogram manipulations
    • Using trk or tck files
    • Tractogram registration
      • Linear transformation
      • Non-linear deformation
      • Complete example
      • Apply back and forth tractogram transformation with the ANTS transformation
    • Tractogram manipulations: logical operations, resampling, filtering
      • The range of possibilities is wide!
      • Preparing data for this tutorial
      • A. Logical operations
      • B. Tractogram resampling
      • C. Tractogram flipping
    • Streamlines manipulation
      • Preparing data for this tutorial
      • Resampling the number of points in each streamline
      • Compressing streamlines
      • Cutting streamlines
  • 5. Bundle segmentation and analysis (tractometry, profilometry)
    • Tractogram Segmentation into bundles
    • Profilometry (statistics on bundles)
      • Defining profilometry
      • References
    • Tractometry (comparing bundles)
    • Creating a bundle template from a chosen population
      • Preparing data for this tutorial
      • Step A. Prepare the bundle of interest in each subject
      • Step B. Quantify inter-subject variability
      • Step C. Combine all subjects into a population template
  • 6. Connectivity
    • Connectivity analyses
      • Examples
  • – From raw data to a complete project –
    • Using bash to loop on subjects
    • Using nextflow
      • Nextflow
      • nf-neuro
      • Tractoflow
    • From raw diffusion to DTI, fODF, and tractogram
      • Preprocessing
      • Reconstruction
      • DTI reconstruction
      • DTI Tractography
      • fODF reconstruction
      • fODF Tractography
      • References
  • – Visualization –
    • Create overlapping slice mosaics
    • Adding data_per_point to tractograms for visualization
  • – Useful utilitary scripts –
    • Using development containers with Visual Studio Code
      • Prerequisites
      • Launching the container
      • Using the container
    • Instructions to write the tsv files “participants.tsv” for the script scil_stats_group_comparison
      • Header
      • Specific row
  • – Reproducing scilpy paper figures –

Modules and API reference

  • Modules
    • scilpy.connectivity package
      • scilpy.connectivity.connectivity module
        • compute_connectivity_matrices_from_hdf5()
        • compute_triu_connectivity_from_labels()
        • multi_proc_compute_connectivity_matrices_from_hdf5()
      • scilpy.connectivity.matrix_tools module
        • apply_reordering()
        • compute_olo()
        • evaluate_functional_graph_measures()
        • evaluate_graph_measures()
        • normalize_matrix_from_parcel()
        • normalize_matrix_from_values()
    • 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
        • OpenCL environment variables
    • scilpy.gradients package
      • scilpy.gradients.bvec_bval_tools module
        • B0ExtractionStrategy
        • check_b0_threshold()
        • check_shells_frf()
        • find_flip_swap_from_order()
        • flip_gradient_axis()
        • 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_stats_in_label()
        • harmonize_labels()
        • 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()
        • find_strides_transform()
        • split_mask_blobs_kmeans()
        • verify_strides()
        • volume_iterator()
      • scilpy.image.volume_b0_synthesis module
        • compute_b0_synthesis()
      • 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()
        • maximum()
        • 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_metrics module
        • estimate_piesno_sigma()
      • 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
        • DataVolume
        • FTODFDataVolume
        • FibertubeDataVolume
    • 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.dvc module
        • get_default_config()
        • pull_from_dvc_repository()
        • pull_package_from_dvc_repository()
        • pull_test_case_package()
      • 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.hdf5 module
        • assert_header_compatible_hdf5()
        • construct_hdf5_from_sft()
        • construct_hdf5_group_from_streamlines()
        • construct_hdf5_header()
        • reconstruct_sft_from_hdf5()
        • reconstruct_streamlines_from_hdf5()
      • scilpy.io.image module
        • assert_same_resolution()
        • get_data_as_mask()
        • load_img()
      • scilpy.io.mti module
        • add_common_args_mti()
        • load_and_verify_mti()
      • scilpy.io.streamlines module
        • check_tracts_same_format()
        • ichunk()
        • 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_surface_spatial_arg()
        • add_tolerance_arg()
        • add_verbose_arg()
        • add_volume_screenshot_args()
        • add_vtk_legacy_arg()
        • 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()
        • convert_stateful_str_to_enum()
        • get_acq_parameters()
        • get_default_screenshotting_data()
        • is_argument_set()
        • 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.maths package
      • scilpy.maths.utils module
        • fit_circle_planar()
    • scilpy.ml package
      • scilpy.ml.bundleparc.attention module
        • have_torch
        • torch
      • scilpy.ml.bundleparc.bundleparcnet module
      • scilpy.ml.bundleparc.encodings module
        • get_emb()
      • scilpy.ml.bundleparc.labels module
        • post_process_labels_continuous()
        • post_process_labels_discrete()
        • post_process_labels_mm()
      • scilpy.ml.bundleparc.predict module
        • post_process_mask()
      • scilpy.ml.bundleparc.utils module
        • download_weights()
        • get_data()
        • get_model()
    • 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
        • 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()
        • is_data_peaks()
    • scilpy.segment package
      • scilpy.segment.bundleseg module
        • BundleSeg
      • scilpy.segment.streamlines module
        • filter_cuboid()
        • filter_ellipsoid()
        • filter_grid_roi()
        • filter_grid_roi_both_ends()
        • 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
        • omega_sigma()
        • pairwise_agreement()
        • ttest_two_matrices()
      • scilpy.stats.stats module
        • verify_group_difference()
        • verify_homoscedasticity()
        • verify_normality()
        • verify_post_hoc()
      • scilpy.stats.utils module
        • data_for_stat
        • 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.fibertube_utils module
        • create_perpendicular()
        • dist_point_segment()
        • dist_segment_segment()
        • point_in_cylinder()
        • rotation_between_vectors_matrix()
        • sample_cylinder()
        • sample_sphere()
        • sphere_cylinder_intersection()
        • streamlines_to_segments()
      • scilpy.tracking.propagator module
        • AbstractPropagator
        • FibertubePropagator
        • ODFPropagator
        • PropagationStatus
        • PropagatorOnSphere
      • scilpy.tracking.rap module
        • RAP
        • RAPContinue
        • RAPGraph
        • RAPSwitch
      • scilpy.tracking.seed module
        • CustomSeedsDispenser
        • FibertubeSeedGenerator
        • SeedGenerator
      • scilpy.tracking.tracker module
        • GPUTracker
        • Tracker
      • scilpy.tracking.utils module
        • TrackingDirection
        • add_mandatory_options_tracking()
        • add_out_options()
        • add_seeding_options()
        • add_tracking_options()
        • add_tracking_ptt_options()
        • compute_max_sf_amplitude()
        • compute_sf_threshold_mask()
        • get_direction_getter()
        • get_global_sf_threshold_mask()
        • 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_map_along_streamlines()
      • scilpy.tractanalysis.bingham_metric_along_streamlines module
        • bingham_metric_map_along_streamlines()
        • bingham_metric_sum_along_streamlines()
      • scilpy.tractanalysis.bundle_operations module
        • compute_bundle_diameter()
        • detect_ushape()
        • get_streamlines_centroid()
        • outliers_removal_using_hierarchical_quickbundles()
        • prune()
        • remove_outliers_qb()
        • uniformize_bundle_sft()
        • uniformize_bundle_sft_using_mask()
      • scilpy.tractanalysis.connectivity_segmentation module
        • compute_connectivity()
        • construct_hdf5_from_connectivity()
        • extract_longest_segments_from_profile()
      • scilpy.tractanalysis.distance_to_centroid module
        • associate_labels()
        • closest_match_to_centroid()
        • compute_distance_map()
        • compute_labels_map_barycenters()
        • correct_labels_jump()
        • find_medoid()
        • masked_manhattan_distance()
        • subdivide_bundles()
      • scilpy.tractanalysis.fixel_density module
        • fixel_density()
        • fixel_maps_to_masks()
      • scilpy.tractanalysis.json_utils module
        • average_dict()
        • merge_dict()
      • scilpy.tractanalysis.mrds_along_streamlines module
        • mrds_metric_sums_along_streamlines()
        • mrds_metrics_along_streamlines()
      • scilpy.tractanalysis.multi_bundle_operations module
        • filter_by_occurrence()
      • scilpy.tractanalysis.reproducibility_measures module
        • approximate_surface_node()
        • binary_classification()
        • compare_bundle_wrapper()
        • compare_volume_wrapper()
        • compute_bundle_adjacency_streamlines()
        • compute_bundle_adjacency_voxel()
        • compute_correlation()
        • compute_dice_streamlines()
        • compute_dice_voxel()
        • compute_fractal_dimension()
        • compute_hausdorff_voxel()
        • tractogram_pairwise_comparison()
      • scilpy.tractanalysis.scoring module
        • Tractometry
        • compute_ae()
        • compute_f1_overlap_overreach()
        • compute_f1_score()
        • compute_tractometry()
        • get_binary_maps()
      • scilpy.tractanalysis.streamlines_metrics module
        • compute_tract_counts_map()
      • scilpy.tractanalysis.todi module
        • TrackOrientationDensityImaging
        • get_sf_from_todi()
        • get_sh_from_todi()
      • 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.voxel_boundary_intersection module
        • subdivide_streamlines_at_voxel_faces()
    • 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.intersection_finder module
        • IntersectionFinder
      • scilpy.tractograms.lazy_tractogram_operations module
        • lazy_concatenate()
        • lazy_streamlines_count()
      • scilpy.tractograms.streamline_and_mask_operations module
        • CuttingStyle
        • compute_streamline_segment()
        • cut_streamlines_between_labels()
        • cut_streamlines_with_mask()
        • get_endpoints_density_map()
        • get_head_tail_density_maps()
      • scilpy.tractograms.streamline_operations module
        • compress_sft()
        • cut_invalid_streamlines()
        • filter_streamlines_by_length()
        • filter_streamlines_by_nb_points()
        • filter_streamlines_by_total_length_per_dim()
        • find_seed_indexes_on_streamlines()
        • generate_matched_points()
        • get_angles()
        • get_streamlines_as_fixed_array()
        • get_streamlines_as_linspaces()
        • get_streamlines_bounding_box()
        • parallel_transport_streamline()
        • remove_loops()
        • remove_loops_and_sharp_turns()
        • remove_overlapping_points_streamlines()
        • remove_sharp_turns_qb()
        • remove_streamlines_with_overlapping_points()
        • resample_streamlines_num_points()
        • resample_streamlines_step_size()
        • smooth_line_gaussian()
        • smooth_line_spline()
      • scilpy.tractograms.tractogram_operations module
        • compress_streamlines_wrapper()
        • concatenate_sft()
        • cut_streamlines_alter()
        • difference()
        • difference_robust()
        • flip_sft()
        • get_axis_flip_vector()
        • intersection()
        • intersection_robust()
        • perform_tractogram_operation_on_lines()
        • perform_tractogram_operation_on_sft()
        • replace_streamlines_alter()
        • shuffle_streamlines()
        • shuffle_streamlines_orientation()
        • split_sft_randomly()
        • split_sft_randomly_per_cluster()
        • split_sft_sequentially()
        • subsample_streamlines_alter()
        • transform_streamlines_alter()
        • transform_warp_sft()
        • trim_streamlines_alter()
        • union()
        • union_robust()
        • upsample_tractogram()
      • scilpy.tractograms.uncompress module
        • streamlines_to_voxel_coordinates()
    • 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.scilpy_bot module
        • prompt_user_for_object()
        • update_matches_and_scores()
      • scilpy.utils.spatial module
        • WorldBoundingBox
        • compute_distance_barycenters()
        • generate_rotation_matrix()
        • get_axis_index()
        • get_axis_name()
        • get_basis_vector_name()
        • get_coordinate_name()
        • voxel_to_world()
        • world_to_voxel()
    • scilpy.viz package
      • scilpy.viz.color module
        • ambiant_occlusion()
        • clip_and_normalize_data_for_cmap()
        • convert_color_names_to_rgb()
        • format_hexadecimal_color_to_rgb()
        • generate_local_coloring()
        • generate_n_colors()
        • get_lookup_table()
        • lut_from_matplotlib_name()
        • prepare_colorbar_figure()
      • scilpy.viz.gradients module
        • build_ms_from_shell_idx()
        • plot_each_shell()
        • plot_proj_shell()
      • scilpy.viz.plot module
        • plot_metrics_stats()
        • plot_residuals()
      • scilpy.viz.screenshot module
        • compose_image()
        • compose_mosaic()
        • screenshot_contour()
        • screenshot_peaks()
        • screenshot_volume()
      • scilpy.viz.slice module
        • create_bingham_slicer()
        • create_contours_slicer()
        • create_odf_slicer()
        • create_peaks_slicer()
        • create_texture_slicer()
      • scilpy.viz.utils module
        • affine_from_offset()
        • check_mosaic_layout()
        • compute_cell_topleft_pos()
  • Scripts
    • scil_NODDI_maps
    • scil_NODDI_priors
    • scil_aodf_metrics
    • scil_bids_validate
    • scil_bingham_metrics
    • scil_btensor_metrics
    • scil_bundle_alter_to_target_dice
    • scil_bundle_clean_qbx_clusters
    • scil_bundle_compute_centroid
    • scil_bundle_compute_endpoints_map
    • scil_bundle_diameter
    • scil_bundle_explore_bundleseg
    • scil_bundle_filter_by_occurrence
    • scil_bundle_fixel_analysis
    • scil_bundle_generate_priors
    • scil_bundle_label_map
    • scil_bundle_mean_fixel_afd
    • scil_bundle_mean_fixel_afd_from_hdf5
    • scil_bundle_mean_fixel_bingham_metric
    • scil_bundle_mean_fixel_mrds_metric
    • scil_bundle_mean_std
    • scil_bundle_pairwise_comparison
    • scil_bundle_reject_outliers
    • scil_bundle_score_many_bundles_one_tractogram
    • scil_bundle_score_same_bundle_many_segmentations
    • scil_bundle_shape_measures
    • scil_bundle_uniformize_endpoints
    • scil_bundle_volume_per_label
    • scil_connectivity_compare_populations
    • scil_connectivity_compute_matrices
    • scil_connectivity_compute_pca
    • scil_connectivity_compute_simple_matrix
    • scil_connectivity_filter
    • scil_connectivity_functional_graph_measures
    • scil_connectivity_hdf5_average_density_map
    • scil_connectivity_math
    • scil_connectivity_normalize
    • scil_connectivity_pairwise_agreement
    • scil_connectivity_print_filenames
    • scil_connectivity_reorder_rois
    • scil_connectivity_structural_graph_measures
    • scil_denoising_nlmeans
    • scil_dki_metrics
    • scil_dti_convert_tensors
    • scil_dti_metrics
    • scil_dwi_apply_bias_field
    • scil_dwi_compute_snr
    • scil_dwi_concatenate
    • scil_dwi_convert_FDF
    • scil_dwi_detect_volume_outliers
    • scil_dwi_extract_b0
    • scil_dwi_extract_shell
    • scil_dwi_powder_average
    • scil_dwi_prepare_eddy_command
    • scil_dwi_prepare_topup_command
    • scil_dwi_reorder_philips
    • scil_dwi_split_by_indices
    • scil_dwi_to_sh
    • scil_fibertube_compute_density
    • scil_fibertube_score_tractogram
    • scil_fibertube_tracking
    • scil_fodf_bundleparc
    • scil_fodf_max_in_ventricles
    • scil_fodf_memsmt
    • scil_fodf_metrics
    • scil_fodf_msmt
    • scil_fodf_ssst
    • scil_fodf_threshold_by_amplitude
    • scil_fodf_to_bingham
    • scil_freewater_maps
    • scil_frf_mean
    • scil_frf_memsmt
    • scil_frf_msmt
    • scil_frf_set_diffusivities
    • scil_frf_ssst
    • scil_get_version
    • scil_gradients_apply_transform
    • scil_gradients_convert
    • scil_gradients_generate_sampling
    • scil_gradients_modify_axes
    • scil_gradients_normalize_bvecs
    • scil_gradients_round_bvals
    • scil_gradients_validate_correct
    • scil_gradients_validate_correct_eddy
    • scil_gradients_validate_sampling
    • scil_header_print_info
    • scil_header_validate_compatibility
    • scil_json_convert_entries_to_xlsx
    • scil_json_harmonize_entries
    • scil_json_merge_entries
    • scil_labels_combine
    • scil_labels_dilate
    • scil_labels_from_mask
    • scil_labels_remove
    • scil_labels_split_volume_by_ids
    • scil_labels_split_volume_from_lut
    • scil_lesions_generate_nawm
    • scil_lesions_harmonize_labels
    • scil_lesions_info
    • scil_mrds_metrics
    • scil_mrds_select_number_of_tensors
    • scil_mti_adjust_B1_header
    • scil_mti_maps_MT
    • scil_mti_maps_ihMT
    • scil_plot_stats_per_point
    • scil_qball_metrics
    • scil_rgb_convert
    • scil_search_keywords
    • scil_sh_convert
    • scil_sh_fusion
    • scil_sh_to_aodf
    • scil_sh_to_rish
    • scil_sh_to_sf
    • scil_stats_group_comparison
    • scil_surface_apply_transform
    • scil_surface_assign_custom_color
    • scil_surface_assign_uniform_color
    • scil_surface_convert
    • scil_surface_create
    • scil_surface_flip
    • scil_surface_smooth
    • scil_tracking_local
    • scil_tracking_local_dev
    • scil_tracking_pft
    • scil_tracking_pft_maps
    • scil_tracking_pft_maps_edit
    • scil_tractogram_apply_transform
    • scil_tractogram_apply_transform_to_hdf5
    • scil_tractogram_assign_custom_color
    • scil_tractogram_assign_uniform_color
    • scil_tractogram_commit
    • scil_tractogram_compress
    • scil_tractogram_compute_TODI
    • scil_tractogram_compute_ae
    • scil_tractogram_compute_density_map
    • scil_tractogram_convert
    • scil_tractogram_convert_hdf5_to_trk
    • scil_tractogram_convert_trk_to_hdf5
    • scil_tractogram_count_streamlines
    • scil_tractogram_cut_streamlines
    • scil_tractogram_detect_loops
    • scil_tractogram_dpp_math
    • scil_tractogram_dps_math
    • scil_tractogram_extract_ushape
    • scil_tractogram_filter_by_anatomy
    • scil_tractogram_filter_by_length
    • scil_tractogram_filter_by_orientation
    • scil_tractogram_filter_by_roi
    • scil_tractogram_filter_by_streamlines_properties
    • scil_tractogram_filter_collisions
    • scil_tractogram_flip
    • scil_tractogram_math
    • scil_tractogram_pairwise_comparison
    • scil_tractogram_print_info
    • scil_tractogram_project_map_to_streamlines
    • scil_tractogram_project_streamlines_to_map
    • scil_tractogram_qbx
    • scil_tractogram_register
    • scil_tractogram_remove_invalid
    • scil_tractogram_resample
    • scil_tractogram_resample_nb_points
    • scil_tractogram_seed_density_map
    • scil_tractogram_segment_connections_from_labels
    • scil_tractogram_segment_with_ROI_and_score
    • scil_tractogram_segment_with_bundleseg
    • scil_tractogram_segment_with_recobundles
    • scil_tractogram_shuffle
    • scil_tractogram_smooth
    • scil_tractogram_split
    • scil_viz_bingham_fit
    • scil_viz_bundle
    • scil_viz_bundle_screenshot_mni
    • scil_viz_bundle_screenshot_mosaic
    • scil_viz_connectivity
    • scil_viz_dti_screenshot
    • scil_viz_fodf
    • scil_viz_gradients_screenshot
    • scil_viz_tractogram_collisions
    • scil_viz_tractogram_seeds
    • scil_viz_tractogram_seeds_3d
    • scil_viz_volume_histogram
    • scil_viz_volume_scatterplot
    • scil_viz_volume_screenshot
    • scil_viz_volume_screenshot_mosaic
    • scil_volume_apply_transform
    • scil_volume_b0_synthesis
    • scil_volume_count_non_zero_voxels
    • scil_volume_crop
    • scil_volume_distance_map
    • scil_volume_flip
    • scil_volume_math
    • scil_volume_pairwise_comparison
    • scil_volume_remove_outliers_ransac
    • scil_volume_resample
    • scil_volume_reshape
    • scil_volume_reslice_to_reference
    • scil_volume_stats_in_ROI
    • scil_volume_stats_in_labels
    • scil_volume_validate_correct_strides
scilpy
  • 2. Reconstructing the local model
  • View page source

2. Reconstructing the local model

This section covers local reconstruction methods in scilpy. They mainly use functions in the reconst module.

  • Single-shell single-tissue fODF (ssst-fODF)
  • Multi-shell multi-tissue fODF (msmt-fODF)
  • Multi-encoding multi-shell multi-tissue fODF (memsmt-fODF)
  • Asymmetric orientation distribution functions (aodf)
  • Estimate Q-ball orientation distribution functions
  • Generating Myelin Indices Maps using Magnetization Transfer Imaging (MTI)
  • Tensor-valued dMRI metrics reconstruction using DIVIDE
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