Scripts
==============

.. toctree::
    :maxdepth: 4

    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_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_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_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_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