scilpy
stable
Scilpy
Modules
Scripts
Documentation
Instructions for tensor-valued dMRI scripts (b-tensor)
Instructions for estimation of bundle diameter
Instructions to write the tsv files “participants.tsv” for the script scil_group_comparison.py
Create overlapping slice mosaics
Using development containers with Visual Studio Code
Instructions for streamlines registration/transformation
scilpy
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Index
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R
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W
A
absolute_value() (in module scilpy.image.volume_math)
AbstractPropagator (class in scilpy.tracking.propagator)
add_b0_thresh_arg() (in module scilpy.io.utils)
add_b0s_to_bvecs() (in module scilpy.gradients.optimize_gradient_sampling)
add_bbox_arg() (in module scilpy.io.utils)
add_compression_arg() (in module scilpy.io.utils)
add_data_as_color_dpp() (in module scilpy.tractograms.dps_and_dpp_management)
add_default_screenshot_args() (in module scilpy.io.utils)
add_filename_suffix() (in module scilpy.utils.filenames)
add_gradient_info() (in module scilpy.io.varian_fdf)
add_input_buffer() (scilpy.gpuparallel.opencl_utils.CLManager method)
add_json_args() (in module scilpy.io.utils)
add_labelmap_screenshot_args() (in module scilpy.io.utils)
add_mandatory_options_tracking() (in module scilpy.tracking.utils)
add_out_options() (in module scilpy.tracking.utils)
add_output_buffer() (scilpy.gpuparallel.opencl_utils.CLManager method)
add_overlays_screenshot_args() (in module scilpy.io.utils)
add_overwrite_arg() (in module scilpy.io.utils)
add_peaks_screenshot_args() (in module scilpy.io.utils)
add_processes_arg() (in module scilpy.io.utils)
add_reference_arg() (in module scilpy.io.utils)
add_seeding_options() (in module scilpy.tracking.utils)
add_sh_basis_args() (in module scilpy.io.utils)
add_skip_b0_check_arg() (in module scilpy.io.utils)
add_sphere_arg() (in module scilpy.io.utils)
add_tolerance_arg() (in module scilpy.io.utils)
add_tracking_options() (in module scilpy.tracking.utils)
add_tracking_ptt_options() (in module scilpy.tracking.utils)
add_verbose_arg() (in module scilpy.io.utils)
add_volume_screenshot_args() (in module scilpy.io.utils)
addition() (in module scilpy.image.volume_math)
adjust_B1_map_header() (in module scilpy.reconst.mti)
adjust_B1_map_intensities() (in module scilpy.reconst.mti)
afd_and_rd_sums_along_streamlines() (in module scilpy.tractanalysis.afd_along_streamlines)
afd_map_along_streamlines() (in module scilpy.tractanalysis.afd_along_streamlines)
affine_from_offset() (in module scilpy.viz.utils)
ALL (scilpy.gradients.bvec_bval_tools.B0ExtractionStrategy attribute)
apply_B1_corr_empiric() (in module scilpy.reconst.mti)
apply_B1_corr_model_based() (in module scilpy.reconst.mti)
apply_bias_field() (in module scilpy.dwi.operations)
apply_olo() (in module scilpy.connectivity.connectivity_tools)
apply_reordering() (in module scilpy.connectivity.connectivity_tools)
apply_transform() (in module scilpy.image.volume_operations)
(in module scilpy.surfaces.surface_operations)
approximate_surface_node() (in module scilpy.tractanalysis.reproducibility_measures)
around() (in module scilpy.image.volume_math)
assert_fsl_options_exist() (in module scilpy.io.utils)
assert_gradients_filenames_valid() (in module scilpy.io.utils)
assert_headers_compatible() (in module scilpy.io.utils)
assert_inputs_exist() (in module scilpy.io.utils)
assert_output_dirs_exist_and_empty() (in module scilpy.io.utils)
assert_outputs_exist() (in module scilpy.io.utils)
assert_overlay_colors() (in module scilpy.io.utils)
assert_roi_radii_format() (in module scilpy.io.utils)
assert_same_resolution() (in module scilpy.io.image)
average_dict() (in module scilpy.tractanalysis.json_utils)
B
B0ExtractionStrategy (class in scilpy.gradients.bvec_bval_tools)
base_10_log() (in module scilpy.image.volume_math)
binary_classification() (in module scilpy.tractanalysis.reproducibility_measures)
bingham_fit_sh() (in module scilpy.reconst.bingham)
bingham_metric_map_along_streamlines() (in module scilpy.tractanalysis.bingham_metric_along_streamlines)
bingham_metric_sum_along_streamlines() (in module scilpy.tractanalysis.bingham_metric_along_streamlines)
bingham_to_peak_direction() (in module scilpy.reconst.bingham)
bingham_to_sf() (in module scilpy.reconst.bingham)
BinghamDistribution (class in scilpy.reconst.bingham)
C
ceil() (in module scilpy.image.volume_math)
check_b0_threshold() (in module scilpy.gradients.bvec_bval_tools)
check_mosaic_layout() (in module scilpy.viz.utils)
check_slice_indices() (in module scilpy.image.utils)
check_tracts_same_format() (in module scilpy.io.streamlines)
(in module scilpy.io.utils)
cl_device_type() (in module scilpy.gpuparallel.opencl_utils)
cleanup() (scilpy.segment.recobundlesx.RecobundlesX method)
CLKernel (class in scilpy.gpuparallel.opencl_utils)
CLManager (class in scilpy.gpuparallel.opencl_utils)
CLManager.OutBuffer (class in scilpy.gpuparallel.opencl_utils)
closing() (in module scilpy.image.volume_math)
code_string (scilpy.gpuparallel.opencl_utils.CLKernel property)
combine_labels() (in module scilpy.image.labels)
compose_image() (in module scilpy.viz.screenshot)
compose_mosaic() (in module scilpy.viz.screenshot)
compress_streamlines_wrapper() (in module scilpy.tractograms.tractogram_operations)
compute_asymmetry_index() (in module scilpy.reconst.aodf)
compute_average_dir() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
compute_bundle_adjacency_streamlines() (in module scilpy.tractanalysis.reproducibility_measures)
compute_bundle_adjacency_voxel() (in module scilpy.tractanalysis.reproducibility_measures)
compute_bvalue_lin_b() (in module scilpy.gradients.optimize_gradient_sampling)
compute_bvalue_lin_q() (in module scilpy.gradients.optimize_gradient_sampling)
compute_cell_topleft_pos() (in module scilpy.viz.utils)
compute_coherence_table_for_transforms() (in module scilpy.reconst.fiber_coherence)
compute_connectivity() (in module scilpy.tractanalysis.tools)
compute_correlation() (in module scilpy.tractanalysis.reproducibility_measures)
compute_dice_streamlines() (in module scilpy.tractanalysis.reproducibility_measures)
compute_dice_voxel() (in module scilpy.tractanalysis.reproducibility_measures)
compute_distance_to_peak() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
compute_dwi_attenuation() (in module scilpy.dwi.operations)
compute_fiber_coherence() (in module scilpy.reconst.fiber_coherence)
compute_fiber_density() (in module scilpy.reconst.bingham)
compute_fiber_fraction() (in module scilpy.reconst.bingham)
compute_fiber_spread() (in module scilpy.reconst.bingham)
compute_fractal_dimension() (in module scilpy.tractanalysis.reproducibility_measures)
compute_lesion_stats() (in module scilpy.utils.metrics_tools)
compute_min_duty_cycle_bruteforce() (in module scilpy.gradients.optimize_gradient_sampling)
compute_msmt_frf() (in module scilpy.reconst.frf)
compute_nifti_bounding_box() (in module scilpy.image.utils)
compute_odd_power_map() (in module scilpy.reconst.aodf)
compute_olo() (in module scilpy.connectivity.connectivity_tools)
compute_peak_power() (in module scilpy.gradients.optimize_gradient_sampling)
compute_ratio_map() (in module scilpy.reconst.mti)
compute_residuals() (in module scilpy.dwi.operations)
compute_residuals_statistics() (in module scilpy.dwi.operations)
compute_rish() (in module scilpy.reconst.sh)
compute_saturation_map() (in module scilpy.reconst.mti)
compute_sh_coefficients() (in module scilpy.reconst.sh)
compute_snr() (in module scilpy.image.volume_operations)
compute_ssst_frf() (in module scilpy.reconst.frf)
compute_todi() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
compute_tract_counts_map() (in module scilpy.tractanalysis.streamlines_metrics)
compute_vectors_norm() (in module scilpy.tractanalysis.todi_util)
concatenate() (in module scilpy.image.volume_math)
concatenate_sft() (in module scilpy.tractograms.tractogram_operations)
convert() (in module scilpy.image.volume_math)
convert_bdelta_to_bshape() (in module scilpy.io.btensor)
convert_bshape_to_bdelta() (in module scilpy.io.btensor)
convert_dps_to_dpp() (in module scilpy.tractograms.dps_and_dpp_management)
convert_freesurfer_into_polydata() (in module scilpy.surfaces.utils)
convert_sh_basis() (in module scilpy.reconst.sh)
convert_sh_to_sf() (in module scilpy.reconst.sh)
convert_tensor_format() (in module scilpy.io.tensor)
convert_tensor_from_dipy_format() (in module scilpy.io.tensor)
convert_tensor_to_dipy_format() (in module scilpy.io.tensor)
correct_b0s_philips() (in module scilpy.gradients.optimize_gradient_sampling)
correct_procpar_intensity() (in module scilpy.io.varian_fdf)
correlation() (in module scilpy.image.volume_math)
cosine_filtering() (in module scilpy.denoise.asym_filtering)
count_non_zero_voxels() (in module scilpy.image.volume_operations)
create_acqparams() (in module scilpy.preprocessing.distortion_correction)
create_index() (in module scilpy.preprocessing.distortion_correction)
create_multi_topup_index() (in module scilpy.preprocessing.distortion_correction)
create_non_zero_norm_bvecs() (in module scilpy.preprocessing.distortion_correction)
crop_data_with_default_cube() (in module scilpy.image.volume_operations)
crop_volume() (in module scilpy.image.volume_operations)
cut_up_cube() (in module scilpy.image.volume_math)
D
data_dictionnary (scilpy.stats.utils.data_for_stat attribute)
data_for_stat (class in scilpy.stats.utils)
DataVolume (class in scilpy.image.volume_space_management)
deprecate_script() (in module scilpy.io.deprecator)
detect_volume_outliers() (in module scilpy.dwi.operations)
difference() (in module scilpy.image.volume_math)
(in module scilpy.tractograms.tractogram_operations)
difference_robust() (in module scilpy.tractograms.tractogram_operations)
dilate_labels() (in module scilpy.image.labels)
dilation() (in module scilpy.image.volume_math)
division() (in module scilpy.image.volume_math)
download_file_from_google_drive() (in module scilpy.io.fetcher)
E
entry_point (scilpy.gpuparallel.opencl_utils.CLKernel property)
erosion() (in module scilpy.image.volume_math)
ERROR (scilpy.tracking.propagator.PropagationStatus attribute)
evaluate() (scilpy.reconst.bingham.BinghamDistribution method)
evaluate_graph_measures() (in module scilpy.connectivity.connectivity_tools)
extract_affine() (in module scilpy.image.utils)
extract_b0() (in module scilpy.dwi.utils)
extract_dwi_shell() (in module scilpy.dwi.utils)
extract_longest_segments_from_profile() (in module scilpy.tractanalysis.tools)
extract_xform() (in module scilpy.surfaces.utils)
F
fetch_data() (in module scilpy.io.fetcher)
filter_cuboid() (in module scilpy.segment.streamlines)
filter_ellipsoid() (in module scilpy.segment.streamlines)
filter_grid_roi() (in module scilpy.segment.streamlines)
filter_grid_roi_both() (in module scilpy.segment.streamlines)
finalize_streamline() (scilpy.tracking.propagator.AbstractPropagator method)
find_order_from_nb_coeff() (in module scilpy.reconst.utils)
FIRST (scilpy.gradients.bvec_bval_tools.B0ExtractionStrategy attribute)
fit_from_model() (in module scilpy.reconst.fodf)
fit_gamma() (in module scilpy.reconst.divide)
flip() (in module scilpy.surfaces.surface_operations)
flip_gradient_sampling() (in module scilpy.gradients.bvec_bval_tools)
flip_LPS() (in module scilpy.surfaces.utils)
flip_sft() (in module scilpy.tractograms.tractogram_operations)
flip_volume() (in module scilpy.image.volume_operations)
floor() (in module scilpy.image.volume_math)
format_raw_header() (in module scilpy.io.varian_fdf)
fsl2mrtrix() (in module scilpy.io.gradients)
G
gamma_fit2metrics() (in module scilpy.reconst.divide)
gaussian_blur() (in module scilpy.image.volume_math)
generate_btensor_input() (in module scilpy.io.btensor)
generate_gradient_sampling() (in module scilpy.gradients.gen_gradient_sampling)
generate_mask_indices_1d() (in module scilpy.tractanalysis.todi_util)
get_acq_parameters() (in module scilpy.io.utils)
get_array_ops() (in module scilpy.image.volume_math)
get_axis_flip_vector() (in module scilpy.tractograms.tractogram_operations)
get_bundle_metrics_mean_std() (in module scilpy.utils.metrics_tools)
get_bundle_metrics_mean_std_per_point() (in module scilpy.utils.metrics_tools)
get_bundle_metrics_profiles() (in module scilpy.utils.metrics_tools)
get_bundles_list() (scilpy.stats.utils.data_for_stat method)
get_data_as_labels() (in module scilpy.image.labels)
get_data_as_mask() (in module scilpy.io.image)
get_data_sample() (scilpy.stats.utils.data_for_stat method)
get_default_screenshotting_data() (in module scilpy.io.utils)
get_dir_to_sphere_id() (in module scilpy.tractanalysis.todi_util)
get_direction_getter() (in module scilpy.tracking.utils)
get_final_pruned_indices() (scilpy.segment.recobundlesx.RecobundlesX method)
get_first_bundle() (scilpy.stats.utils.data_for_stat method)
get_first_metric() (scilpy.stats.utils.data_for_stat method)
get_first_participant() (scilpy.stats.utils.data_for_stat method)
get_flatten() (scilpy.reconst.bingham.BinghamDistribution method)
get_gain() (in module scilpy.io.varian_fdf)
get_group_data_sample() (in module scilpy.stats.utils)
get_groups_dictionnary() (scilpy.stats.utils.data_for_stat method)
get_groups_list() (scilpy.stats.utils.data_for_stat method)
get_image_ops() (in module scilpy.image.volume_math)
get_indices_1d() (in module scilpy.tractanalysis.todi_util)
get_lut_dir() (in module scilpy.image.labels)
get_mask() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
get_maximas() (in module scilpy.reconst.utils)
get_metrics_list() (scilpy.stats.utils.data_for_stat method)
get_new_gtab_order() (in module scilpy.gradients.utils)
get_next_n_pos() (scilpy.tracking.seed.SeedGenerator method)
get_next_pos() (scilpy.tracking.seed.SeedGenerator method)
get_next_real_point() (in module scilpy.tractanalysis.quick_tools)
get_operations_doc() (in module scilpy.image.volume_math)
get_participant_attributes_list() (scilpy.stats.utils.data_for_stat method)
get_participants_list() (scilpy.stats.utils.data_for_stat method)
get_previous_real_point() (in module scilpy.tractanalysis.quick_tools)
get_segments_dir_and_norm() (in module scilpy.tractanalysis.todi_util)
get_segments_mid_pts_positions() (in module scilpy.tractanalysis.todi_util)
get_segments_vectors() (in module scilpy.tractanalysis.todi_util)
get_sh() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
get_sh_order_and_fullness() (in module scilpy.reconst.utils)
get_sphere_neighbours() (in module scilpy.reconst.utils)
get_stats_in_label() (in module scilpy.image.labels)
get_synb0_template_path() (in module scilpy.io.fetcher)
get_tdi() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
get_testing_files_dict() (in module scilpy.io.fetcher)
get_theta() (in module scilpy.tracking.utils)
get_todi() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
get_todi_shape() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
get_value_at_coordinate() (scilpy.image.volume_space_management.DataVolume method)
get_value_at_idx() (scilpy.image.volume_space_management.DataVolume method)
get_values_list() (scilpy.stats.utils.data_for_stat method)
get_vectors_dir_and_norm() (in module scilpy.tractanalysis.todi_util)
get_vectors_dir_and_norm_rel_to_center() (in module scilpy.tractanalysis.todi_util)
get_ventricles_max_fodf() (in module scilpy.reconst.fodf)
GPUTacker (class in scilpy.tracking.tracker)
grid_intersections() (in module scilpy.tractanalysis.grid_intersections)
I
ichunk() (in module scilpy.io.streamlines)
identify_shells() (in module scilpy.gradients.bvec_bval_tools)
init_generator() (scilpy.tracking.seed.SeedGenerator method)
intersection() (in module scilpy.image.volume_math)
(in module scilpy.tractograms.tractogram_operations)
intersection_robust() (in module scilpy.tractograms.tractogram_operations)
invert() (in module scilpy.image.volume_math)
is_argument_set() (in module scilpy.io.streamlines)
is_coordinate_in_bound() (scilpy.image.volume_space_management.DataVolume method)
is_idx_in_bound() (scilpy.image.volume_space_management.DataVolume method)
is_normalized_bvecs() (in module scilpy.gradients.bvec_bval_tools)
L
lazy_concatenate() (in module scilpy.tractograms.lazy_tractogram_operations)
lazy_streamlines_count() (in module scilpy.tractograms.lazy_tractogram_operations)
link_bundles_and_reference() (in module scilpy.io.utils)
load_dpp_files_as_dpp() (in module scilpy.io.streamlines)
load_dps_files_as_dps() (in module scilpy.io.streamlines)
load_fdf() (in module scilpy.io.varian_fdf)
load_img() (in module scilpy.io.image)
load_matrix_in_any_format() (in module scilpy.io.utils)
load_tractogram_with_reference() (in module scilpy.io.streamlines)
lower_clip() (in module scilpy.image.volume_math)
lower_threshold() (in module scilpy.image.volume_math)
lower_threshold_eq() (in module scilpy.image.volume_math)
lower_threshold_otsu() (in module scilpy.image.volume_math)
M
maps_from_sh() (in module scilpy.reconst.sh)
mask_todi() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
MEAN (scilpy.gradients.bvec_bval_tools.B0ExtractionStrategy attribute)
mean() (in module scilpy.image.volume_math)
merge_dict() (in module scilpy.tractanalysis.json_utils)
merge_labels_into_mask() (in module scilpy.io.image)
merge_metrics() (in module scilpy.image.volume_operations)
min_dist_to_centroid() (in module scilpy.tractanalysis.distance_to_centroid)
module
scilpy.connectivity.connectivity_tools
scilpy.denoise.asym_filtering
scilpy.dwi.operations
scilpy.dwi.utils
scilpy.gpuparallel.opencl_utils
scilpy.gradients.bvec_bval_tools
scilpy.gradients.gen_gradient_sampling
scilpy.gradients.optimize_gradient_sampling
scilpy.gradients.utils
scilpy.image.labels
scilpy.image.reslice
scilpy.image.utils
scilpy.image.volume_math
scilpy.image.volume_operations
scilpy.image.volume_space_management
scilpy.io.btensor
scilpy.io.deprecator
scilpy.io.fetcher
scilpy.io.gradients
scilpy.io.image
scilpy.io.streamlines
scilpy.io.tensor
scilpy.io.utils
scilpy.io.varian_fdf
scilpy.preprocessing.distortion_correction
scilpy.reconst.aodf
scilpy.reconst.bingham
scilpy.reconst.divide
scilpy.reconst.fiber_coherence
scilpy.reconst.fodf
scilpy.reconst.frf
scilpy.reconst.mti
scilpy.reconst.sh
scilpy.reconst.utils
scilpy.segment.models
scilpy.segment.recobundlesx
scilpy.segment.streamlines
scilpy.segment.voting_scheme
scilpy.stats.matrix_stats
scilpy.stats.stats
scilpy.stats.utils
scilpy.surfaces.surface_operations
scilpy.surfaces.utils
scilpy.tracking.propagator
scilpy.tracking.seed
scilpy.tracking.tracker
scilpy.tracking.utils
scilpy.tractanalysis.afd_along_streamlines
scilpy.tractanalysis.bingham_metric_along_streamlines
scilpy.tractanalysis.distance_to_centroid
scilpy.tractanalysis.grid_intersections
scilpy.tractanalysis.json_utils
scilpy.tractanalysis.quick_tools
scilpy.tractanalysis.reproducibility_measures
scilpy.tractanalysis.streamlines_metrics
scilpy.tractanalysis.todi
scilpy.tractanalysis.todi_util
scilpy.tractanalysis.tools
scilpy.tractograms.dps_and_dpp_management
scilpy.tractograms.lazy_tractogram_operations
scilpy.tractograms.tractogram_operations
scilpy.utils.filenames
scilpy.utils.metrics_tools
scilpy.viz.screenshot
scilpy.viz.utils
mrtrix2fsl() (in module scilpy.io.gradients)
multiplication() (in module scilpy.image.volume_math)
N
natural_log() (in module scilpy.image.volume_math)
normalize_bvecs() (in module scilpy.gradients.bvec_bval_tools)
normalize_matrix_from_parcel() (in module scilpy.connectivity.connectivity_tools)
normalize_matrix_from_values() (in module scilpy.connectivity.connectivity_tools)
normalize_max() (in module scilpy.image.volume_math)
normalize_metric() (in module scilpy.image.volume_operations)
normalize_sum() (in module scilpy.image.volume_math)
normalize_todi_per_voxel() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
normalize_vectors() (in module scilpy.tractanalysis.todi_util)
O
ODFPropagator (class in scilpy.tracking.propagator)
omega_sigma() (in module scilpy.stats.matrix_stats)
opening() (in module scilpy.image.volume_math)
P
p_normalize_vectors() (in module scilpy.tractanalysis.todi_util)
parse_sh_basis_arg() (in module scilpy.io.utils)
parser_color_type() (in module scilpy.io.utils)
peak_direction() (scilpy.reconst.bingham.BinghamDistribution method)
peaks_from_sh() (in module scilpy.reconst.sh)
perform_correlation_on_endpoints() (in module scilpy.tractograms.dps_and_dpp_management)
perform_operation_dpp_to_dps() (in module scilpy.tractograms.dps_and_dpp_management)
perform_operation_on_dpp() (in module scilpy.tractograms.dps_and_dpp_management)
perform_tractogram_operation_on_lines() (in module scilpy.tractograms.tractogram_operations)
perform_tractogram_operation_on_sft() (in module scilpy.tractograms.tractogram_operations)
plot_metrics_stats() (in module scilpy.utils.metrics_tools)
pre_filtering_for_geometrical_shape() (in module scilpy.segment.streamlines)
prepare_backward() (scilpy.tracking.propagator.AbstractPropagator method)
(scilpy.tracking.propagator.PropagatorOnSphere method)
prepare_forward() (scilpy.tracking.propagator.AbstractPropagator method)
(scilpy.tracking.propagator.ODFPropagator method)
process_contrast_map() (in module scilpy.reconst.mti)
project_dpp_to_map() (in module scilpy.tractograms.dps_and_dpp_management)
project_map_to_streamlines() (in module scilpy.tractograms.dps_and_dpp_management)
propagate() (scilpy.tracking.propagator.AbstractPropagator method)
PropagationStatus (class in scilpy.tracking.propagator)
PropagatorOnSphere (class in scilpy.tracking.propagator)
prune_far_from_model() (scilpy.segment.recobundlesx.RecobundlesX method)
psf_from_sphere() (in module scilpy.tractanalysis.todi_util)
py_fspecial_gauss() (in module scilpy.reconst.mti)
R
random_uniform_on_sphere() (in module scilpy.gradients.utils)
ranged_type() (in module scilpy.io.utils)
read_directory() (in module scilpy.io.varian_fdf)
read_file() (in module scilpy.io.varian_fdf)
read_info_from_mb_bdo() (in module scilpy.io.utils)
RecobundlesX (class in scilpy.segment.recobundlesx)
recognize() (scilpy.segment.recobundlesx.RecobundlesX method)
reconstruct_streamlines() (in module scilpy.io.streamlines)
reconstruct_streamlines_from_memmap() (in module scilpy.io.streamlines)
redirect_stdout_c() (in module scilpy.io.utils)
register_image() (in module scilpy.image.volume_operations)
remove_labels() (in module scilpy.image.labels)
remove_outliers_ransac() (in module scilpy.image.volume_operations)
remove_similar_streamlines() (in module scilpy.segment.models)
replace_frf() (in module scilpy.reconst.frf)
resample_volume() (in module scilpy.image.volume_operations)
reset_data() (scilpy.tracking.propagator.AbstractPropagator method)
reshape_to_3d() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
reslice() (in module scilpy.image.reslice)
round_bvals_to_shell() (in module scilpy.gradients.bvec_bval_tools)
run() (scilpy.gpuparallel.opencl_utils.CLManager method)
S
sample_distribution() (in module scilpy.tracking.utils)
save_babel() (in module scilpy.io.varian_fdf)
save_gradient_sampling_fsl() (in module scilpy.io.gradients)
save_gradient_sampling_mrtrix() (in module scilpy.io.gradients)
save_matrix_in_any_format() (in module scilpy.io.utils)
save_tractogram() (in module scilpy.io.streamlines)
(in module scilpy.tracking.utils)
scilpy.connectivity.connectivity_tools
module
scilpy.denoise.asym_filtering
module
scilpy.dwi.operations
module
scilpy.dwi.utils
module
scilpy.gpuparallel.opencl_utils
module
scilpy.gradients.bvec_bval_tools
module
scilpy.gradients.gen_gradient_sampling
module
scilpy.gradients.optimize_gradient_sampling
module
scilpy.gradients.utils
module
scilpy.image.labels
module
scilpy.image.reslice
module
scilpy.image.utils
module
scilpy.image.volume_math
module
scilpy.image.volume_operations
module
scilpy.image.volume_space_management
module
scilpy.io.btensor
module
scilpy.io.deprecator
module
scilpy.io.fetcher
module
scilpy.io.gradients
module
scilpy.io.image
module
scilpy.io.streamlines
module
scilpy.io.tensor
module
scilpy.io.utils
module
scilpy.io.varian_fdf
module
scilpy.preprocessing.distortion_correction
module
scilpy.reconst.aodf
module
scilpy.reconst.bingham
module
scilpy.reconst.divide
module
scilpy.reconst.fiber_coherence
module
scilpy.reconst.fodf
module
scilpy.reconst.frf
module
scilpy.reconst.mti
module
scilpy.reconst.sh
module
scilpy.reconst.utils
module
scilpy.segment.models
module
scilpy.segment.recobundlesx
module
scilpy.segment.streamlines
module
scilpy.segment.voting_scheme
module
scilpy.stats.matrix_stats
module
scilpy.stats.stats
module
scilpy.stats.utils
module
scilpy.surfaces.surface_operations
module
scilpy.surfaces.utils
module
scilpy.tracking.propagator
module
scilpy.tracking.seed
module
scilpy.tracking.tracker
module
scilpy.tracking.utils
module
scilpy.tractanalysis.afd_along_streamlines
module
scilpy.tractanalysis.bingham_metric_along_streamlines
module
scilpy.tractanalysis.distance_to_centroid
module
scilpy.tractanalysis.grid_intersections
module
scilpy.tractanalysis.json_utils
module
scilpy.tractanalysis.quick_tools
module
scilpy.tractanalysis.reproducibility_measures
module
scilpy.tractanalysis.streamlines_metrics
module
scilpy.tractanalysis.todi
module
scilpy.tractanalysis.todi_util
module
scilpy.tractanalysis.tools
module
scilpy.tractograms.dps_and_dpp_management
module
scilpy.tractograms.lazy_tractogram_operations
module
scilpy.tractograms.tractogram_operations
module
scilpy.utils.filenames
module
scilpy.utils.metrics_tools
module
scilpy.viz.screenshot
module
scilpy.viz.utils
module
ScilpyExpiredDeprecation
screenshot_contour() (in module scilpy.viz.screenshot)
screenshot_peaks() (in module scilpy.viz.screenshot)
screenshot_volume() (in module scilpy.viz.screenshot)
SeedGenerator (class in scilpy.tracking.seed)
set_define() (scilpy.gpuparallel.opencl_utils.CLKernel method)
set_todi() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
shuffle_streamlines() (in module scilpy.tractograms.tractogram_operations)
single_recognize() (in module scilpy.segment.voting_scheme)
smooth_B1_map() (in module scilpy.reconst.mti)
smooth_to_fwhm() (in module scilpy.image.volume_operations)
smooth_todi_dir() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
smooth_todi_spatial() (scilpy.tractanalysis.todi.TrackOrientationDensityImaging method)
split_labels() (in module scilpy.image.labels)
split_mask_blobs_kmeans() (in module scilpy.image.utils)
split_name_with_nii() (in module scilpy.utils.filenames)
split_sft_randomly() (in module scilpy.tractograms.tractogram_operations)
split_sft_randomly_per_cluster() (in module scilpy.tractograms.tractogram_operations)
split_sft_sequentially() (in module scilpy.tractograms.tractogram_operations)
std() (in module scilpy.image.volume_math)
str_to_axis_index() (in module scilpy.gradients.bvec_bval_tools)
streamlines_in_mask() (in module scilpy.segment.streamlines)
streamlines_to_endpoints() (in module scilpy.tractanalysis.todi_util)
streamlines_to_memmap() (in module scilpy.io.streamlines)
streamlines_to_pts_dir_norm() (in module scilpy.tractanalysis.todi_util)
streamlines_to_segments() (in module scilpy.tractanalysis.todi_util)
subtraction() (in module scilpy.image.volume_math)
swap_gradient_axis() (in module scilpy.gradients.bvec_bval_tools)
swap_sampling_eddy() (in module scilpy.gradients.optimize_gradient_sampling)
T
threshold_map() (in module scilpy.reconst.mti)
tqdm_if_verbose() (in module scilpy.tracking.utils)
track() (scilpy.tracking.tracker.Tracker method)
Tracker (class in scilpy.tracking.tracker)
TrackingDirection (class in scilpy.tracking.utils)
TrackOrientationDensityImaging (class in scilpy.tractanalysis.todi)
tractogram_pairwise_comparison() (in module scilpy.tractanalysis.reproducibility_measures)
transform_dwi() (in module scilpy.image.volume_operations)
transform_warp_sft() (in module scilpy.tractograms.tractogram_operations)
ttest_two_matrices() (in module scilpy.stats.matrix_stats)
U
unified_filtering() (in module scilpy.denoise.asym_filtering)
union() (in module scilpy.image.volume_math)
(in module scilpy.tractograms.tractogram_operations)
union_robust() (in module scilpy.tractograms.tractogram_operations)
update_input_buffer() (scilpy.gpuparallel.opencl_utils.CLManager method)
update_output_buffer() (scilpy.gpuparallel.opencl_utils.CLManager method)
upper_clip() (in module scilpy.image.volume_math)
upper_threshold() (in module scilpy.image.volume_math)
upper_threshold_eq() (in module scilpy.image.volume_math)
upper_threshold_otsu() (in module scilpy.image.volume_math)
upsample_tractogram() (in module scilpy.tractograms.tractogram_operations)
V
validate_nbr_processes() (in module scilpy.io.utils)
validate_sh_basis_choice() (in module scilpy.io.utils)
validation_participant_id() (scilpy.stats.utils.data_for_stat method)
verify_compatibility_with_reference_sft() (in module scilpy.io.streamlines)
verify_compression_th() (in module scilpy.io.utils)
verify_data_vs_sh_order() (in module scilpy.reconst.sh)
verify_failed_voxels_shm_coeff() (in module scilpy.reconst.fodf)
verify_frf_files() (in module scilpy.reconst.fodf)
verify_group_difference() (in module scilpy.stats.stats)
verify_homoscedasticity() (in module scilpy.stats.stats)
verify_normality() (in module scilpy.stats.stats)
verify_post_hoc() (in module scilpy.stats.stats)
verify_seed_options() (in module scilpy.tracking.utils)
verify_streamline_length_options() (in module scilpy.tracking.utils)
visualise_distribution() (in module scilpy.stats.utils)
volume_iterator() (in module scilpy.image.utils)
VotingScheme (class in scilpy.segment.voting_scheme)
vox_to_idx() (scilpy.image.volume_space_management.DataVolume static method)
voxmm_to_idx() (scilpy.image.volume_space_management.DataVolume method)
voxmm_to_vox() (scilpy.image.volume_space_management.DataVolume method)
W
weighted_mean_std() (in module scilpy.utils.metrics_tools)
write_csv_from_json() (in module scilpy.stats.utils)
write_current_dictionnary() (in module scilpy.stats.utils)
write_gradient_information() (in module scilpy.io.varian_fdf)
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