Index

A

absolutepath() (spinalcordtoolbox.image.Image property) add_entry() (in module spinalcordtoolbox.reports.qc) add_slice() (spinalcordtoolbox.reports.slice.Slice static method) add_suffix() (in module spinalcordtoolbox.image)

aggregate_per_slice_or_level() (in module spinalcordtoolbox.aggregate_slicewise) all_refspace_strings() (in module spinalcordtoolbox.image) average_vert_length (spinalcordtoolbox.types.Centerline attribute) Axial (class in spinalcordtoolbox.reports.slice)

B

BoundingBox (class in spinalcordtoolbox.cropping)

bspline() (in module spinalcordtoolbox.centerline.curve_fitting)

C

center_of_mass() (in module spinalcordtoolbox.vertebrae.core) Centerline (class in spinalcordtoolbox.types) centerline2roi() (in module spinalcordtoolbox.centerline.optic) change_orientation() (in module spinalcordtoolbox.image) (spinalcordtoolbox.image.Image method) change_shape() (in module spinalcordtoolbox.image) (spinalcordtoolbox.image.Image method) change_type() (in module spinalcordtoolbox.image) (spinalcordtoolbox.image.Image method) check_backend() (in module spinalcordtoolbox.deepseg_gm.deepseg_gm) check_dim() (in module spinalcordtoolbox.image) check_labels() (in module spinalcordtoolbox.aggregate_slicewise) clean_labeled_segmentation() (in module spinalcordtoolbox.vertebrae.core) compare_centerline() (spinalcordtoolbox.types.Centerline method) compute_coordinate_system() (spinalcordtoolbox.types.Centerline method) compute_corr_3d() (in module spinalcordtoolbox.vertebrae.core) compute_dice() (in module spinalcordtoolbox.image)

compute_mtr() (in module spinalcordtoolbox.qmri.mt) compute_mtsat() (in module spinalcordtoolbox.qmri.mt) compute_shape() (in module spinalcordtoolbox.process_seg) compute_similarity() (in module spinalcordtoolbox.math) compute_vertebral_distribution() (spinalcordtoolbox.types.Centerline method) concat_data() (in module spinalcordtoolbox.image) concat_warp2d() (in module spinalcordtoolbox.image) concatenate_along_4th_dimension() (in module spinalcordtoolbox.math) convert() (in module spinalcordtoolbox.image) Coordinate (class in spinalcordtoolbox.types) CoordinateValue (class in spinalcordtoolbox.types) copy_qform_from_ref() (spinalcordtoolbox.image.Image method) correlation() (in module spinalcordtoolbox.math) create_label_z() (in module spinalcordtoolbox.vertebrae.core) create_model() (in module spinalcordtoolbox.deepseg_gm.model) crop() (spinalcordtoolbox.reports.slice.Slice static method) crop_center() (in module spinalcordtoolbox.deepseg_gm.deepseg_gm) CroppedRegion (class in spinalcordtoolbox.deepseg_gm.deepseg_gm)

D

DataResource (class in spinalcordtoolbox.deepseg_gm.deepseg_gm) denoise_nlmeans() (in module spinalcordtoolbox.math) detect_centerline() (in module spinalcordtoolbox.centerline.optic) dice() (in module spinalcordtoolbox.math) dice_coef() (in module spinalcordtoolbox.deepseg_gm.model)

dice_coef_loss() (in module spinalcordtoolbox.deepseg_gm.model) diff_between_list_or_int() (in module spinalcordtoolbox.aggregate_slicewise) dilate() (in module spinalcordtoolbox.math) display() (spinalcordtoolbox.types.Centerline method) divide_after_removing_zero() (in module spinalcordtoolbox.qmri.mt)

E

empty_like() (in module spinalcordtoolbox.image)

erode() (in module spinalcordtoolbox.math) extract_metric() (in module spinalcordtoolbox.aggregate_slicewise)

F

fill_holes_2d() (in module spinalcordtoolbox.deepseg_sc.postprocessing) find_and_sort_coord() (in module spinalcordtoolbox.centerline.core) find_nearest_index() (spinalcordtoolbox.types.Centerline method) find_zmin_zmax() (in module spinalcordtoolbox.image) FitResults (class in spinalcordtoolbox.centerline.core) fix_orientation() (in module spinalcordtoolbox.process_seg) folder() (in module spinalcordtoolbox.deepseg.models)

func_bin() (in module spinalcordtoolbox.aggregate_slicewise) func_map() (in module spinalcordtoolbox.aggregate_slicewise) func_max() (in module spinalcordtoolbox.aggregate_slicewise) func_ml() (in module spinalcordtoolbox.aggregate_slicewise) func_std() (in module spinalcordtoolbox.aggregate_slicewise) func_sum() (in module spinalcordtoolbox.aggregate_slicewise) func_wa() (in module spinalcordtoolbox.aggregate_slicewise)

G

generate_output_file() (in module spinalcordtoolbox.image) generate_qc() (in module spinalcordtoolbox.reports.qc) get_center() (spinalcordtoolbox.reports.slice.Axial method) get_center_spit() (spinalcordtoolbox.reports.slice.Sagittal method) get_centerline() (in module spinalcordtoolbox.centerline.core) get_closest_to_relative_position() (spinalcordtoolbox.types.Centerline method) get_dim() (spinalcordtoolbox.reports.slice.Axial method) (spinalcordtoolbox.reports.slice.Sagittal method) (spinalcordtoolbox.reports.slice.Slice method) get_dimension() (in module spinalcordtoolbox.image) get_directions() (spinalcordtoolbox.image.Image method) get_distance_from_plane() (spinalcordtoolbox.types.Centerline method) get_file_label() (in module spinalcordtoolbox.metadata) get_file_path() (spinalcordtoolbox.deepseg_gm.deepseg_gm.DataResource method) get_in_plane_coordinates() (spinalcordtoolbox.types.Centerline method) get_indiv_label_info() (in module spinalcordtoolbox.metadata) get_json_data_from_path() (in module spinalcordtoolbox.reports.qc) get_metadata() (in module spinalcordtoolbox.deepseg.models)

get_minmax() (spinalcordtoolbox.cropping.BoundingBox method) get_name() (spinalcordtoolbox.reports.slice.Axial method) (spinalcordtoolbox.reports.slice.Sagittal method) (spinalcordtoolbox.reports.slice.Slice method) get_nearest_plane() (spinalcordtoolbox.types.Centerline method) get_orientation() (in module spinalcordtoolbox.image) get_plan_parameters() (spinalcordtoolbox.types.Centerline method) get_point_from_index() (spinalcordtoolbox.types.Centerline method) get_projected_coordinates_on_plane() (spinalcordtoolbox.types.Centerline method) get_slice() (spinalcordtoolbox.reports.slice.Axial method) (spinalcordtoolbox.reports.slice.Sagittal method) (spinalcordtoolbox.reports.slice.Slice method) get_slices_from_vertebral_levels() (in module spinalcordtoolbox.template) get_values() (spinalcordtoolbox.image.Image method) get_vertebral_level_from_slice() (in module spinalcordtoolbox.template) get_z_and_disc_values_from_label() (in module spinalcordtoolbox.vertebrae.core) getCoordinatesAveragedByValue() (spinalcordtoolbox.image.Image method) getNonZeroCoordinates() (spinalcordtoolbox.image.Image method)

H

highlight_pmj() (spinalcordtoolbox.reports.qc.QcImage method)

I

Image (class in spinalcordtoolbox.image) InfoLabel (class in spinalcordtoolbox.metadata) install_default_models() (in module spinalcordtoolbox.deepseg.models)

install_model() (in module spinalcordtoolbox.deepseg.models) interpolate_from_image() (spinalcordtoolbox.image.Image method) is_valid() (in module spinalcordtoolbox.deepseg.models)

K

keep_largest_object() (in module spinalcordtoolbox.deepseg_sc.postprocessing)

L

label_centerline() (spinalcordtoolbox.reports.qc.QcImage method) label_discs() (in module spinalcordtoolbox.vertebrae.core) label_segmentation() (in module spinalcordtoolbox.vertebrae.core) label_utils() (spinalcordtoolbox.reports.qc.QcImage method) label_vert() (in module spinalcordtoolbox.vertebrae.core) label_vertebrae() (spinalcordtoolbox.reports.qc.QcImage method) LabelStruc (class in spinalcordtoolbox.aggregate_slicewise)

laplacian() (in module spinalcordtoolbox.math) line_angle() (spinalcordtoolbox.reports.qc.QcImage method) linear() (in module spinalcordtoolbox.centerline.curve_fitting) list_tasks() (in module spinalcordtoolbox.deepseg.models) listed_seg() (spinalcordtoolbox.reports.qc.QcImage method) load() (spinalcordtoolbox.metadata.InfoLabel method) loadFromPath() (spinalcordtoolbox.image.Image method)

M

make_a_string() (in module spinalcordtoolbox.aggregate_slicewise) make_content_path() (spinalcordtoolbox.reports.qc.QcReport method) mean() (spinalcordtoolbox.image.Image method) merge_dict() (in module spinalcordtoolbox.aggregate_slicewise) Metric (class in spinalcordtoolbox.aggregate_slicewise) module spinalcordtoolbox.aggregate_slicewise spinalcordtoolbox.centerline.core spinalcordtoolbox.centerline.curve_fitting spinalcordtoolbox.centerline.optic spinalcordtoolbox.cropping spinalcordtoolbox.deepseg.core spinalcordtoolbox.deepseg.models spinalcordtoolbox.deepseg_gm.deepseg_gm spinalcordtoolbox.deepseg_gm.model spinalcordtoolbox.deepseg_sc.postprocessing spinalcordtoolbox.image spinalcordtoolbox.math spinalcordtoolbox.metadata spinalcordtoolbox.process_seg spinalcordtoolbox.qmri.mt spinalcordtoolbox.reports.qc spinalcordtoolbox.reports.slice spinalcordtoolbox.resampling spinalcordtoolbox.template spinalcordtoolbox.types spinalcordtoolbox.utils spinalcordtoolbox.vertebrae.core

mosaic() (spinalcordtoolbox.reports.slice.Slice method) mutual_information() (in module spinalcordtoolbox.math)

N

nan_fill() (spinalcordtoolbox.reports.slice.Slice static method)

no_seg_seg() (spinalcordtoolbox.reports.qc.QcImage method)

O

orientation_string_nib2sct() (in module spinalcordtoolbox.image)

orientation_string_sct2nib() (in module spinalcordtoolbox.image)

P

pad() (spinalcordtoolbox.deepseg_gm.deepseg_gm.CroppedRegion method) ParamCenterline (class in spinalcordtoolbox.centerline.core) Params (class in spinalcordtoolbox.reports.qc)

permute() (spinalcordtoolbox.types.Coordinate method) Point (class in spinalcordtoolbox.types) polyfit_1d() (in module spinalcordtoolbox.centerline.curve_fitting) post_processing_volume_wise() (in module spinalcordtoolbox.deepseg_sc.postprocessing)

Q

QcImage (class in spinalcordtoolbox.reports.qc)

QcReport (class in spinalcordtoolbox.reports.qc)

R

read_label_file() (in module spinalcordtoolbox.metadata) resample_file() (in module spinalcordtoolbox.resampling)

resample_nib() (in module spinalcordtoolbox.resampling) round_and_clip() (in module spinalcordtoolbox.centerline.core) round_up_to_odd() (in module spinalcordtoolbox.centerline.curve_fitting)

S

Sagittal (class in spinalcordtoolbox.reports.slice) save() (spinalcordtoolbox.image.Image method) (spinalcordtoolbox.metadata.InfoLabel method) save_as_csv() (in module spinalcordtoolbox.aggregate_slicewise) segment_file() (in module spinalcordtoolbox.deepseg_gm.deepseg_gm) segment_nifti() (in module spinalcordtoolbox.deepseg.core) segment_volume() (in module spinalcordtoolbox.deepseg_gm.deepseg_gm) single() (spinalcordtoolbox.reports.slice.Slice method) Slice (class in spinalcordtoolbox.reports.slice) Slicer (class in spinalcordtoolbox.image) SlicerMany (class in spinalcordtoolbox.image) SlicerOneAxis (class in spinalcordtoolbox.image) smooth() (in module spinalcordtoolbox.math) smooth1d() (in module spinalcordtoolbox.centerline.curve_fitting) spatial_crop() (in module spinalcordtoolbox.image) spinalcordtoolbox.aggregate_slicewise module spinalcordtoolbox.centerline.core module spinalcordtoolbox.centerline.curve_fitting module spinalcordtoolbox.centerline.optic module spinalcordtoolbox.cropping module spinalcordtoolbox.deepseg.core module spinalcordtoolbox.deepseg.models module spinalcordtoolbox.deepseg_gm.deepseg_gm module

spinalcordtoolbox.deepseg_gm.model module spinalcordtoolbox.deepseg_sc.postprocessing module spinalcordtoolbox.image module spinalcordtoolbox.math module spinalcordtoolbox.metadata module spinalcordtoolbox.process_seg module spinalcordtoolbox.qmri.mt module spinalcordtoolbox.reports.qc module spinalcordtoolbox.reports.slice module spinalcordtoolbox.resampling module spinalcordtoolbox.template module spinalcordtoolbox.types module spinalcordtoolbox.utils module spinalcordtoolbox.vertebrae.core module split_img_data() (in module spinalcordtoolbox.image) splitext() (in module spinalcordtoolbox.image) StandardizationTransform (class in spinalcordtoolbox.deepseg_gm.deepseg_gm)

T

template() (spinalcordtoolbox.reports.qc.QcImage method) threshold_predictions() (in module spinalcordtoolbox.deepseg_gm.deepseg_gm)

to_dtype() (in module spinalcordtoolbox.image) transfo_phys2pix() (spinalcordtoolbox.image.Image method) transfo_pix2phys() (spinalcordtoolbox.image.Image method)

U

update_description_file() (spinalcordtoolbox.reports.qc.QcReport method)

V

vertebral_detection() (in module spinalcordtoolbox.vertebrae.core)

vertical_line() (spinalcordtoolbox.reports.qc.QcImage method) VolumeStandardizationTransform (class in spinalcordtoolbox.deepseg_gm.deepseg_gm)

Z

zeros_like() (in module spinalcordtoolbox.image)