Getting started
Documentation & Tutorials
Modules and API reference
compute_connectivity_matrices_from_hdf5()
compute_triu_connectivity_from_labels()
multi_proc_compute_connectivity_matrices_from_hdf5()
apply_reordering()
compute_olo()
evaluate_functional_graph_measures()
evaluate_graph_measures()
normalize_matrix_from_parcel()
normalize_matrix_from_values()
cosine_filtering()
unified_filtering()
apply_bias_field()
compute_dwi_attenuation()
compute_residuals()
compute_residuals_statistics()
detect_volume_outliers()
extract_b0()
extract_dwi_shell()
CLKernel
CLManager
cl_device_type()
B0ExtractionStrategy
check_b0_threshold()
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()
energy_comparison()
generate_gradient_sampling()
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()
get_new_gtab_order()
random_uniform_on_sphere()
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()
reslice()
check_slice_indices()
compute_nifti_bounding_box()
extract_affine()
find_strides_transform()
split_mask_blobs_kmeans()
verify_strides()
volume_iterator()
compute_b0_synthesis()
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()
estimate_piesno_sigma()
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()
DataVolume
FTODFDataVolume
FibertubeDataVolume
convert_bdelta_to_bshape()
convert_bshape_to_bdelta()
generate_btensor_input()
ScilpyExpiredDeprecation
deprecate_script()
get_default_config()
pull_from_dvc_repository()
pull_package_from_dvc_repository()
pull_test_case_package()
download_file_from_google_drive()
fetch_data()
get_synb0_template_path()
get_testing_files_dict()
fsl2mrtrix()
mrtrix2fsl()
save_gradient_sampling_fsl()
save_gradient_sampling_mrtrix()
assert_header_compatible_hdf5()
construct_hdf5_from_sft()
construct_hdf5_group_from_streamlines()
construct_hdf5_header()
reconstruct_sft_from_hdf5()
reconstruct_streamlines_from_hdf5()
assert_same_resolution()
get_data_as_mask()
load_img()
add_common_args_mti()
load_and_verify_mti()
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()
convert_tensor_format()
convert_tensor_from_dipy_format()
convert_tensor_to_dipy_format()
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()
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()
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()
add_gradient_info()
correct_procpar_intensity()
format_raw_header()
get_gain()
load_fdf()
read_directory()
read_file()
save_babel()
write_gradient_information()
fit_circle_planar()
have_torch
torch
get_emb()
post_process_labels_continuous()
post_process_labels_discrete()
post_process_labels_mm()
post_process_mask()
download_weights()
get_data()
get_model()
create_acqparams()
create_index()
create_multi_topup_index()
create_non_zero_norm_bvecs()
compute_asymmetry_index()
compute_odd_power_map()
BinghamDistribution
bingham_fit_sh()
bingham_to_peak_direction()
bingham_to_sf()
compute_fiber_density()
compute_fiber_fraction()
compute_fiber_spread()
fit_gamma()
gamma_fit2metrics()
compute_coherence_table_for_transforms()
compute_fiber_coherence()
fit_from_model()
get_ventricles_max_fodf()
verify_failed_voxels_shm_coeff()
verify_frf_files()
compute_msmt_frf()
compute_ssst_frf()
replace_frf()
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()
compute_rish()
compute_sh_coefficients()
convert_sh_basis()
convert_sh_to_sf()
maps_from_sh()
peaks_from_sh()
verify_data_vs_sh_order()
find_order_from_nb_coeff()
get_maximas()
get_sh_order_and_fullness()
get_sphere_neighbours()
BundleSeg
filter_cuboid()
filter_ellipsoid()
filter_grid_roi()
filter_grid_roi_both_ends()
streamlines_in_mask()
compute_endpoint_masks()
compute_masks_from_bundles()
segment_tractogram_from_roi()
VotingScheme
single_recognize()
single_recognize_parallel()
omega_sigma()
pairwise_agreement()
ttest_two_matrices()
verify_group_difference()
verify_homoscedasticity()
verify_normality()
verify_post_hoc()
data_for_stat
get_group_data_sample()
visualise_distribution()
write_csv_from_json()
write_current_dictionnary()
flip()
convert_freesurfer_into_polydata()
flip_surfaces_axes()
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()
AbstractPropagator
FibertubePropagator
ODFPropagator
PropagationStatus
PropagatorOnSphere
RAP
RAPContinue
RAPGraph
CustomSeedsDispenser
FibertubeSeedGenerator
SeedGenerator
GPUTacker
Tracker
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()
tqdm_if_verbose()
verify_seed_options()
verify_streamline_length_options()
afd_map_along_streamlines()
bingham_metric_map_along_streamlines()
bingham_metric_sum_along_streamlines()
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()
compute_connectivity()
construct_hdf5_from_connectivity()
extract_longest_segments_from_profile()
associate_labels()
closest_match_to_centroid()
compute_labels_map_barycenters()
correct_labels_jump()
find_medoid()
masked_manhattan_distance()
subdivide_bundles()
fixel_density()
fixel_maps_to_masks()
average_dict()
merge_dict()
mrds_metric_sums_along_streamlines()
mrds_metrics_along_streamlines()
filter_by_occurrence()
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()
compute_f1_overlap_overreach()
compute_f1_score()
compute_tractometry()
get_binary_maps()
compute_tract_counts_map()
TrackOrientationDensityImaging
get_sf_from_todi()
get_sh_from_todi()
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()
subdivide_streamlines_at_voxel_faces()
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()
IntersectionFinder
lazy_concatenate()
lazy_streamlines_count()
CuttingStyle
compute_streamline_segment()
cut_streamlines_between_labels()
cut_streamlines_with_mask()
get_endpoints_density_map()
get_head_tail_density_maps()
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()
compress_streamlines_wrapper()
concatenate_sft()
cut_streamlines_alter()
difference_robust()
flip_sft()
get_axis_flip_vector()
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_robust()
upsample_tractogram()
streamlines_to_voxel_coordinates()
add_filename_suffix()
split_name_with_nii()
compute_lesion_stats()
get_bundle_metrics_mean_std()
get_bundle_metrics_mean_std_per_point()
get_bundle_metrics_profiles()
weighted_mean_std()
prompt_user_for_object()
update_matches_and_scores()
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()
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()
build_ms_from_shell_idx()
plot_each_shell()
plot_proj_shell()
plot_metrics_stats()
plot_residuals()
compose_image()
compose_mosaic()
screenshot_contour()
screenshot_peaks()
screenshot_volume()
create_bingham_slicer()
create_contours_slicer()
create_odf_slicer()
create_peaks_slicer()
create_texture_slicer()
affine_from_offset()
check_mosaic_layout()
compute_cell_topleft_pos()
This section covers voulume manipulation methods in scilpy. Most of the functions in those scripts are included in the volume module.