tract_querier.tract_label_indices¶

Classes

`tract_querier.tract_label_indices.BoundingBox`	Bounding box assuming RAS coordinate system
`tract_querier.tract_label_indices.TractographySpatialIndexing`(...)	This class implements a mutual spatial indexing of

Functions

`tract_querier.tract_label_indices.compute_label_bounding_boxes`(...)
`tract_querier.tract_label_indices.compute_label_crossings`(...)
`tract_querier.tract_label_indices.compute_label_endings`(...)
`tract_querier.tract_label_indices.compute_label_endings_start_end`(...)
`tract_querier.tract_label_indices.compute_tract_bounding_boxes`(tracts)
`tract_querier.tract_label_indices.compute_tract_label_indices`(...)

class tract_querier.tract_label_indices.TractographySpatialIndexing(tractography, image, affine_ijk_2_ras, length_threshold, crossing_threshold)[source]¶

This class implements a mutual spatial indexing of an labeled image and a tractography

Parameters:

tractography : Tractography

Tractography object

image : array_like, 3-dimensional

a piecewise constant 3D image or image of labels

affine_ijk_2_ras : array_like, $4 \times 4$

the affine transform of each IJK coordinate on the image to RAS space

length_threshold : float

minimum length in mm of a tract to be considered in the indexing

crossing_threshold : float

the ratio of a tract that needs to be inside a label to be considered that it crosses it

Attributes

tractography	(`Tractography`) Tractography object
image	(array_like, 3-dimensional) a piecewise constant 3D image or image of labels
affine_ijk_2_ras	(array_like, $4 \times 4$ ) the affine transform of each IJK coordinate on the image to RAS space
length_threshold	(float) minimum length in mm of a tract to be considered in the indexing
crossing_threshold	(float) the ratio of a tract that needs to be inside a label to be considered that it crosses it
crossing_tracts_labels	(dict of sets) Dictionary indexed by tract number of the labels traversed by the tract
crossing_labels_tracts	(dict of sets) Dictionary indexed by label number of the tracts traversing the labels
ending_tracts_labels	((dict of int, dict of int)) Dictionary of each endpoint of the tracts indexed by tract number and containing the label at which the endpoint is
ending_labels_tracts	((dict of sets, dict of sets)) Dictionary of each endpoint of the tracts indexed by label number and containing the tracts at which the endpoint in the label is
tract_endpoints_pos	(array_like of $N\times 2 \times 3$ where) $N$ is the number of tracts Contains the position of both endpoints of each tract